This code will load the model information, generate the model definition, and run the model estimation using FSL
In [6]:
import nipype.algorithms.modelgen as model # model generation
from nipype.interfaces import fsl, ants
from nipype.interfaces.base import Bunch
import os,json,glob,sys
import numpy
import nibabel
import nilearn.plotting
%matplotlib inline
import matplotlib.pyplot as plt
datadir='/home/vagrant/data/ds000114_R2.0.1/'
results_dir = os.path.abspath("../../results")
if not os.path.exists(results_dir):
os.mkdir(results_dir)
from nipype.caching import Memory
mem = Memory(base_dir='.')
print('Using data from',datadir)
Using data from /home/vagrant/data/ds000114_R2.0.1/
In [7]:
from bids.grabbids import BIDSLayout
layout = BIDSLayout(datadir)
layout.get(type="bold", task="fingerfootlips", session="test", extensions="nii.gz")[0].filename
Out[7]:
'/home/vagrant/data/ds000114_R2.0.1/sub-01/ses-test/func/sub-01_ses-test_task-fingerfootlips_bold.nii.gz'
In [92]:
import pandas as pd
events = pd.read_csv(os.path.join(datadir, "task-fingerfootlips_events.tsv"), sep="\t")
events
Out[92]:
onset
duration
weight
trial_type
0
10
15.0
1
Finger
1
40
15.0
1
Foot
2
70
15.0
1
Lips
3
100
15.0
1
Finger
4
130
15.0
1
Foot
5
160
15.0
1
Lips
6
190
15.0
1
Finger
7
220
15.0
1
Foot
8
250
15.0
1
Lips
9
280
15.0
1
Finger
10
310
15.0
1
Foot
11
340
15.0
1
Lips
12
370
15.0
1
Finger
13
400
15.0
1
Foot
14
430
15.0
1
Lips
In [93]:
for trial_type in events.trial_type.unique():
print(events[events.trial_type == trial_type])
onset duration weight trial_type
0 10 15.0 1 Finger
3 100 15.0 1 Finger
6 190 15.0 1 Finger
9 280 15.0 1 Finger
12 370 15.0 1 Finger
onset duration weight trial_type
1 40 15.0 1 Foot
4 130 15.0 1 Foot
7 220 15.0 1 Foot
10 310 15.0 1 Foot
13 400 15.0 1 Foot
onset duration weight trial_type
2 70 15.0 1 Lips
5 160 15.0 1 Lips
8 250 15.0 1 Lips
11 340 15.0 1 Lips
14 430 15.0 1 Lips
In [94]:
events[events.trial_type == 'Finger'].duration
Out[94]:
0 15.0
3 15.0
6 15.0
9 15.0
12 15.0
Name: duration, dtype: float64
In [95]:
source_epi = layout.get(type="bold", task="fingerfootlips", session="test", extensions="nii.gz")[5]
confounds = pd.read_csv(os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_confounds.tsv"%(source_epi.subject,
source_epi.session)),
sep="\t", na_values="n/a")
info = [Bunch(conditions=['Finger',
'Foot',
'Lips'],
onsets=[list(events[events.trial_type == 'Finger'].onset-10),
list(events[events.trial_type == 'Foot'].onset-10),
list(events[events.trial_type == 'Lips'].onset-10)],
durations=[list(events[events.trial_type == 'Finger'].duration),
list(events[events.trial_type == 'Foot'].duration),
list(events[events.trial_type == 'Lips'].duration)],
regressors=[list(confounds.FramewiseDisplacement.fillna(0)[4:]),
list(confounds.aCompCor0[4:]),
list(confounds.aCompCor1[4:]),
list(confounds.aCompCor2[4:]),
list(confounds.aCompCor3[4:]),
list(confounds.aCompCor4[4:]),
list(confounds.aCompCor5[4:]),
],
regressor_names=['FramewiseDisplacement',
'aCompCor0',
'aCompCor1',
'aCompCor2',
'aCompCor3',
'aCompCor4',
'aCompCor5',])
]
skip = mem.cache(fsl.ExtractROI)
skip_results = skip(in_file=os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_preproc.nii.gz"%(source_epi.subject,
source_epi.session)),
t_min=4, t_size=-1)
s = model.SpecifyModel()
s.inputs.input_units = 'secs'
s.inputs.functional_runs = skip_results.outputs.roi_file
s.inputs.time_repetition = layout.get_metadata(source_epi.filename)["RepetitionTime"]
s.inputs.high_pass_filter_cutoff = 128.
s.inputs.subject_info = info
specify_model_results = s.run()
s.inputs
170216-19:47:30,476 workflow INFO:
Executing node 2173ff0bacc206ded70e35bfa7c6900d in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/2173ff0bacc206ded70e35bfa7c6900d
170216-19:47:30,487 workflow INFO:
Collecting precomputed outputs
Out[95]:
event_files = <undefined>
functional_runs = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/2173ff0bacc206ded70e35bfa7c6900d/sub-06_ses-test_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_preproc_roi.nii.gz']
high_pass_filter_cutoff = 128.0
ignore_exception = False
input_units = secs
outlier_files = <undefined>
realignment_parameters = <undefined>
subject_info = [Bunch(conditions=['Finger', 'Foot', 'Lips'], durations=[[15.0, 15.0, 15.0, 15.0, 15.0], [15.0, 15.0, 15.0, 15.0, 15.0], [15.0, 15.0, 15.0, 15.0, 15.0]], onsets=[[0, 90, 180, 270, 360], [30, 120, 210, 300, 390], [60, 150, 240, 330, 420]], regressor_names=['FramewiseDisplacement', 'aCompCor0', 'aCompCor1', 'aCompCor2', 'aCompCor3', 'aCompCor4', 'aCompCor5'], regressors=[[0.16517459999999987, 0.16393550000000012, 0.060880000000000101, 0.099227999999999969, 0.092637999999999998, 0.058773500000000013, 0.08213899999999992, 0.07065919999999988, 0.059915799999999887, 0.040129600000000071, 0.087915000000000007, 0.53722140000000007, 0.37261459999999996, 0.15609944999999992, 0.20615815000000001, 0.11306650000000006, 0.78650280000000006, 0.33794455000000001, 0.19718554999999999, 0.081222700000000064, 0.047395350000000003, 0.070689999999999906, 0.054125800000000064, 0.15142230000000007, 0.044283699999999912, 0.10846885000000006, 0.13043414999999989, 0.11277090000000012, 0.078479199999999971, 0.068545650000000014, 0.090304000000000023, 0.050125399999999966, 0.10289699999999996, 0.097612349999999959, 0.15440522999999992, 0.16629848000000008, 0.047173899999999921, 0.075661450000000019, 0.060555500000000026, 0.11385728499999992, 0.035190245000000016, 0.034913249999999889, 0.16059369999999998, 0.053874784999999939, 0.13936081500000005, 0.069495279999999979, 0.11866974000000002, 0.22484146499999999, 0.16623668500000002, 0.097093499999999958, 0.071083899999999992, 0.022817399999999998, 0.11770249999999995, 0.10296874999999993, 0.081075800000000031, 0.069871350000000026, 0.097311499999999981, 0.068844000000000002, 0.046394900000000051, 0.10897365000000001, 0.14090870000000005, 0.11000940000000001, 0.1242501, 0.081413930000000051, 0.11753373000000004, 0.33189583, 0.29748943, 0.099371550000000003, 0.15874460000000001, 0.031603550000000015, 0.072232499999999977, 0.098253499999999994, 0.044037400000000011, 0.077632900000000019, 0.08363969999999997, 0.062188, 0.042488799999999986, 0.070169919999999997, 0.066629280000000013, 0.049232600000000022, 0.11020055400000001, 0.084599653999999969, 0.1351793, 0.097900799999999968, 0.76502095999999986, 0.055104880000000016, 0.10674817000000003, 0.07610355000000002, 0.054521396999999992, 0.15498364700000006, 0.12887514000000005, 0.088985495000000012, 0.077271466000000011, 0.039910559000000026, 0.13350717999999998, 0.071568700000000041, 0.15256744, 0.077055039999999977, 0.064590849999999991, 0.079980369999999981, 0.13742771000000004, 0.45459030000000011, 0.34766205000000011, 0.089609850000000019, 0.068456299999999942, 0.12760249000000001, 0.21788115999999999, 0.066572549999999994, 0.076563999999999979, 0.085570700000000069, 0.049431350000000013, 0.062972300000000009, 0.12426387, 0.25134267999999993, 0.23470850000000004, 0.29123424999999997, 0.13132495, 0.14487375000000008, 0.090303149999999957, 0.040195349999999984, 0.13619029999999999, 0.10077524999999997, 0.030785014999999964, 0.043871825600000053, 0.092358780600000023, 0.095606379999999963, 0.50843034999999992, 0.38368105000000002, 0.26847809999999994, 0.16101379999999998, 0.055101251500000031, 0.38141630150000011, 0.07587644999999997, 0.07810818999999998, 0.085004510000000061, 0.071288850000000001, 0.16647020000000001, 0.48020154999999998, 0.52059655000000005, 0.11314972000000002, 0.10985348, 0.0822349, 0.027236200000000002, 0.075436249999999969, 0.049020550000000031, 0.064593599999999987, 0.055595855, 0.10057375500000004, 0.16430800000000007, 0.12434174999999995, 0.11541970000000006, 0.089557699999999976, 0.10095553, 0.15160693, 0.065574600000000011, 0.14775870000000002, 0.37812014999999999, 0.17141424999999999, 0.51002879999999995, 0.38465404229999994, 0.2141633077, 0.20916519, 0.040236029999999964, 0.13361334000000002, 0.11888422, 0.079965549999999969, 0.037992100000000001, 0.093608399999999994, 0.097055589999999969, 0.069386785000000006, 0.078603724999999999, 0.22082002000000001, 0.16740896999999999, 0.092821599999999976, 0.036417100000000015, 0.064079649999999974, 0.12254188000000002, 0.13889573, 0.087809074999999973, 0.0], [-0.029787337399999999, -0.027126343000000001, -0.051203401099999997, -0.029387428700000006, -0.0125039872, -0.032945181099999998, -0.046301911000000001, -0.019149111699999999, -0.00022791200000000001, -0.016521002, -0.021603886100000001, -0.021797721999999999, -0.019423610099999999, -0.035296345899999998, -0.0520776238, -0.0479258901, -0.041302992699999999, -0.023178171599999998, -0.0059673935999999999, -0.0090065806999999991, -0.0158546169, -0.011554428500000002, -0.0170745268, -0.0014300235000000001, -0.016433731699999999, -0.036652581099999998, -0.025225791099999999, -0.0086260180000000009, 0.00089371890000000003, -0.0140987341, -0.0111827943, -0.0051167748000000004, -0.0013633545000000002, 0.0052061965999999999, 0.0112013254, 0.0159769869, -0.0099001982999999995, -0.0118203708, -0.016784696599999999, -0.0190336862, 0.0074874809999999998, 0.00072439240000000005, -0.01266427, -0.043328152699999997, -0.0134611448, -0.0046127210000000002, 0.0087336259999999995, 0.0055675204000000004, -0.0033516797, -0.039493255099999999, -0.023383822799999999, -0.020578691199999999, -0.017104728700000002, -0.017042326100000001, -0.0171798339, -0.011711685600000001, -0.0151463233, -0.0066473607000000004, 0.028155579100000001, 0.014461842000000001, -0.0057811999999999994, -0.030671530200000002, 0.0233856541, 0.027137187600000001, 0.0027355431, -0.029965167400000006, -0.041082093100000001, 0.032954683800000002, 0.036213154300000001, 0.0068314183999999998, -0.0145182781, -0.0234055284, -0.0056675579, -0.0091387602000000002, -0.021040238500000003, -0.0190979854, -0.030881145700000001, -0.040717703100000002, -0.0070509555000000017, 0.0096555003999999993, 0.0022529939999999999, -0.0083846658999999994, 0.0006370414, -0.0018562305999999999, -0.0083701631999999991, -0.0095969987999999992, -0.024719947499999999, -0.018858894399999999, -0.020594366100000001, -0.036767015700000003, -0.0042097018, -0.012692601699999998, 0.013887185999999999, 0.028031830899999999, 0.025839508399999999, -0.0228585826, -0.031313985799999999, -0.0194732273, 0.0143758514, 0.0048750848999999999, 0.0033111809999999998, -0.0081179001000000004, -0.013139334900000001, 0.0187201179, 0.036244090899999998, 0.0087434086000000005, -0.027991180599999999, -0.032419889799999997, -0.0148870284, -0.0046234036999999997, -0.035570123199999998, 0.0030580484000000004, -0.0098039713000000004, -0.031142192499999999, -0.034851765899999998, -0.019690035200000001, -0.0010344396, 0.017458019799999999, 0.030648072799999999, -0.0001594919, -0.011257111699999999, 0.0028793618999999999, -0.0104290393, -0.021593099800000001, -0.0028101565, 0.00029135240000000001, 0.013979288100000001, -0.010283092400000001, 0.021765751699999999, 0.032106944700000001, 0.0278205742, -0.0068209759999999994, -0.0041961221000000005, 0.0131831525, 0.039940756800000005, 0.048781098799999999, 0.033303576299999998, 0.013995385500000001, 1.00128e-05, 0.011426144900000001, 0.025093135200000002, 0.0154904073, 0.0160871413, 0.0065396095999999994, 0.0073776600000000003, 0.0040491609000000003, 0.0085823131000000007, 0.0130497748, 0.0031480835, 0.0102042212, 0.022641664300000003, 0.0020726693000000002, -0.0074258218000000003, 0.0198901901, 0.0137436678, 0.019989295800000001, -0.0123828047, -0.0055813805000000001, 0.0031051718000000002, -0.0073085403000000002, 0.019825193200000001, 0.007844199100000001, -0.0016119959000000001, 0.0045174580999999998, -0.0052795825999999999, 0.0035846697000000002, 0.0026223156999999999, -0.0072809410999999996, -0.0188892908, -0.021967029300000003, -0.0074360664, 0.016340041200000002, 0.0092994983999999999, 0.0050949348999999996, 0.0101891308, 0.018061509999999999, -0.0030783376999999998, 0.0040098661000000004, 0.0040712748, 0.0051473747000000004], [-0.11578609550000001, -0.11033201049999999, -0.13184946450000001, -0.1083028318, -0.14154735710000002, -0.097049770199999996, -0.078814153400000003, -0.033135085500000001, -0.065707416699999993, -0.056181931800000001, 0.0037981006999999998, -0.045334739200000002, -0.037686229299999999, -0.066403508, -0.014811630500000001, -0.055983364400000006, -0.030131254400000002, -0.092650565500000004, -0.057167333000000001, -0.062745490400000006, -0.095996972900000005, -0.081538373999999997, -0.0595359684, -0.090958995000000001, -0.074927759699999999, -0.075817856900000008, -0.065191184900000004, -0.080211726600000005, -0.058069516699999997, -0.044871359800000003, -0.025595149300000002, -0.031200974400000001, -0.025603879500000003, -0.044005765099999997, 0.010709205899999999, -0.08651006289999999, -0.0313382829, -0.053144728000000002, -0.040695838400000003, -0.056464030900000003, -0.018979006199999999, -0.010694827299999999, -0.041911852400000005, -0.0256989904, -0.016764023200000002, -0.012492543700000001, 0.017311740400000001, 0.012392200500000001, 0.011430644199999999, 0.0056269149999999997, 0.0037507486000000001, 0.021414425899999999, 0.0033740032000000001, 0.022157377200000002, 0.072229329299999992, 0.076203672400000005, 0.083738073199999999, 0.066722911600000004, 0.098248535600000006, 0.089100361300000014, 0.0647743286, 0.055879892200000003, 0.081797537000000003, 0.097366012299999999, 0.070988143599999998, 0.1095221712, 0.038573830199999999, 0.075535826100000009, 0.1043039211, 0.088186438200000009, 0.094055337200000005, 0.10001068809999999, 0.1001776481, 0.087814330800000007, 0.069547605099999993, 0.080782699499999999, 0.0497086126, 0.069903318499999992, 0.094297064900000005, 0.10313191770000001, 0.1069187456, 0.098721393399999996, 0.092960586499999998, 0.1047134316, 0.089920491800000002, 0.083591216799999993, 0.093164941700000004, 0.097155287100000029, 0.1090778017, 0.083052290799999998, 0.099911218699999998, 0.1090115426, 0.1002036025, 0.1051859901, 0.085804895399999997, 0.070457387400000002, 0.094383590000000003, 0.091018304800000005, 0.079144049399999999, 0.093223580900000005, 0.074378128700000004, 0.062544964999999994, 0.076695570300000002, 0.068709455000000003, 0.070666179800000006, 0.083111602399999998, 0.0831870901, 0.065317177199999993, 0.098568640799999996, 0.1138259428, 0.092283988600000005, 0.13315728960000001, 0.084943374299999999, 0.1046313691, 0.054119090799999998, 0.045099328700000003, 0.030244684399999999, 0.012823961199999999, 0.001153875, 0.0200313014, 0.069875332999999998, 0.046684835600000002, 0.051367755799999998, 0.089491664200000001, 0.071209344199999997, 0.032757561300000002, 0.026681101499999998, 0.0057181161999999997, -0.0449169918, -0.033839602400000002, -0.0072282469999999984, -0.034467928600000003, 0.023200504100000002, 0.026235793600000001, -0.0044818636999999998, 0.021459207099999999, -0.0064161162000000004, 0.036030704199999999, -0.011061182899999999, -0.067271571900000007, -0.038878969100000001, -0.071556390300000008, -0.053168290999999999, -0.0748732909, -0.040954178799999998, -0.048706621500000005, -0.024741187400000003, -0.0083679918999999998, -0.038465797400000001, -0.056105933900000002, -0.076491032900000006, -0.0486496134, -0.056590667699999986, -0.031246646699999998, -0.0477910603, -0.0271649443, -0.034462728300000002, -0.093014857899999998, -0.048675283200000002, -0.034235977200000003, -0.029940166000000001, -0.027637978399999999, -0.049107534699999997, -0.077140022699999991, -0.057391339100000001, -0.1069909416, -0.1128300461, -0.10240887379999999, -0.093708472099999995, -0.086002103800000007, -0.11304430209999999, -0.1070386651, -0.1025451473, -0.098752571799999994, -0.089242138000000013, -0.1116983156, -0.1286271957, -0.1102951774, -0.090843521999999996, -0.118746754], [-0.043665168600000005, -0.023456332399999998, -0.111557805, -0.089852424800000011, 0.020268793300000001, -0.070056082500000005, -0.13751253520000001, -0.0688094385, 0.049053064, -0.0089621049000000001, -0.058545419600000002, -0.0051941388999999999, 0.013400086, -0.058772034700000003, -0.099423656999999999, 0.018319964099999999, -0.032620704900000005, 0.071989016399999994, 0.079231102900000003, 0.035226325500000003, 0.025298902000000002, 0.029206158900000001, 0.0023409002, 0.019851566300000002, -0.014889274100000001, -0.054149570700000003, -0.038566477299999999, 0.029424544800000001, 0.074693129400000002, 0.062337480200000003, 0.037235119400000002, 0.068623961900000002, 0.082706671400000001, 0.1035792001, 0.1087149622, 0.0963407233, 0.0293220498, 0.0337554495, 0.012204878799999999, -0.026385650399999998, 0.098574713999999994, 0.099156304599999995, 0.043832177799999997, -0.045191459100000005, -0.0037288979, 0.081102371699999995, 0.099170194599999997, 0.060068886699999997, 0.069264459, -0.091921315300000001, -0.096615101699999997, -0.071791723899999993, -0.056051367999999997, -0.0212800517, -0.032656801700000002, 0.0017030395999999999, -0.0225531034, 0.036743984, 0.0785967271, 0.085955064999999997, 0.020236456900000001, -0.0552988814, 0.1237584675, 0.15628387869999999, 0.081089345300000004, -0.068737483899999993, -0.1035512296, 0.1291314247, 0.1639554902, 0.087722150200000001, 0.015497091100000001, -0.0313658333, -0.0047461561000000001, -0.025719046299999999, -0.037287955300000002, -0.041648262599999999, -0.032525126699999997, -0.093925459700000005, -0.0212541428, 0.037226790799999999, 0.033569019800000002, 0.0058225723000000004, -0.0090722948999999997, -0.0288112653, -0.0055826785000000004, -0.094358979999999995, -0.1072290248, -0.10299388600000001, -0.095187802000000002, -0.123070209, -0.082477436399999993, -0.070556431099999997, 0.057542889799999997, 0.087661770500000014, 0.1317806889, -0.092239402999999998, -0.12903026770000001, -0.077387913700000005, 0.033607365299999997, 0.0071549218999999997, -0.0057052679000000007, -0.010611686499999998, -0.058048979400000013, 0.044008441299999999, 0.14705772449999999, 0.082967952900000003, -0.035898470000000002, -0.1030555447, -0.0091946987999999997, 0.0061509567000000006, -0.093117539599999993, -0.0470495701, -0.061059726699999997, -0.17514563759999999, -0.13765940300000001, -0.1090784243, -0.0018178946, 0.082412683600000008, 0.069640501300000004, 0.060713937099999997, 0.013354006000000002, -0.0351947632, -0.065259077200000001, -0.063526000999999999, -0.017872758400000001, 0.0048745390999999994, 0.076179711900000002, -0.079807353600000006, 0.1013434805, 0.15062043429999999, 0.14653245509999999, 0.0027660550999999999, 0.0050799779999999998, 0.034754966300000002, 0.16529902960000001, 0.189010758, 0.13000816339999999, 0.062552986399999996, 0.014708109699999999, 0.0043166204000000003, 0.056987154200000001, 0.1095495032, 0.0237509144, 0.0073927202999999999, 0.033764830499999995, 0.036187904100000001, 0.067494682400000006, 0.033898066900000003, 0.0446869243, 0.032630381200000003, 0.050287891900000006, 0.0033095849999999999, -0.090864377999999996, 0.0324372718, 0.023764179999999999, 0.0203472338, -0.090009762100000029, -0.13665239099999998, -0.012958247500000001, -0.066000156099999999, 0.065349927000000002, 0.026656258299999999, -0.00084562299999999999, 0.039218171099999997, -0.0523503409, -0.061417817899999998, -0.041345517999999998, -0.054234041699999999, -0.106185896, -0.14667681869999999, -0.1004454821, 0.036625834900000001, -0.07266498099999999, 0.0053669273000000002, -0.0153679018, 0.045926711699999997, -0.060106823500000003, -0.051659126100000001, -0.028506134900000001, 0.047404745800000002], [0.075484539400000009, 0.051970740000000001, 0.1081095066, 0.058485828600000012, 0.07509964429999999, 0.078467751500000002, 0.08569157849999999, 0.031383950000000001, 0.107092983, 0.081163667800000006, 0.016514192, 0.018845444900000001, 0.0058696238999999999, 0.034631121399999999, -0.029372344900000007, 0.0026657746000000003, -0.029178926300000001, 0.049222093500000001, -0.012602898100000001, 0.0049887038, 0.068243836200000005, 0.042205456799999999, 0.0395021157, -0.032707368600000002, 0.016506371699999998, 0.00051754209999999999, -0.0097818343000000002, 0.0067880667000000004, -0.038791527499999999, -0.0062421559999999996, -0.054415894800000003, -0.033569113800000001, -0.077847032499999996, -0.042737903000000001, -0.045491804499999997, 0.0036748899000000001, -0.037361994500000002, -0.033058712900000002, -0.0127874219, -0.053061296900000006, -0.087986511400000009, -0.087899171999999998, -0.011856074499999999, -0.013668868799999999, -0.068436166800000003, -0.091519600899999998, -0.052638073100000002, -0.047321748400000002, -0.064420665799999999, -0.095045061099999995, -0.089299780399999987, -0.037877491200000002, -0.1045627708, -0.056433084299999998, -0.11523098900000001, -0.1102722642, -0.0071816982999999999, -0.065964233600000005, -0.1070282558, -0.049884525399999997, -0.080273038099999999, -0.049368531799999997, -0.0192125769, -0.0612922459, -0.078051598200000002, -0.010404421699999999, -0.022326148099999998, -0.064131227599999993, -0.093163928199999996, -0.0017902447999999999, -0.038206398599999997, -0.021230858700000001, 0.0066938414, -0.063842255199999989, -0.1138231214, -0.091482947699999997, -0.045925984900000001, -0.060422803999999997, -0.11528220760000001, -0.066928209699999991, -0.049043913600000003, -0.039479979999999998, -0.02364571, -0.055364891999999999, -0.1172049307, -0.099368592899999997, -0.1057920889, -0.033143603399999999, -0.015954881899999999, -0.059465847500000002, -0.042409538500000003, -0.013116216399999998, 0.0240477344, 0.043119971799999997, 0.025333285800000001, 0.104277439, 0.029985935500000001, 0.030066171100000001, 0.072326588299999994, 0.053612286600000003, 0.10322658480000001, 0.075521283099999989, -0.016219361000000002, 0.064107777800000001, -0.0063349786, 0.052388420599999999, 0.084808665000000005, 0.080719463700000008, 0.039399481299999997, 0.070897079000000002, 0.072733165500000002, 0.063010492000000001, 0.054295482700000001, 0.16498216979999999, 0.15436226419999999, 0.21103221389999999, 0.14999855619999999, 0.1249106054, 0.1390854869, 0.15684560450000001, 0.038908014800000001, 0.15751792980000001, 0.093810383400000003, 0.091865609700000003, 0.044202943299999999, -0.00093279609999999998, 0.033075921100000003, 0.08251327230000001, 0.1533646108, 0.13407653289999999, 0.044328932600000003, 0.1034653161, 0.0072221158999999984, 0.0176752981, 0.0062559915000000004, -0.0026099008999999999, -0.0023552435000000001, 0.081497684900000006, 0.078826838600000004, 0.081149658499999999, 0.018007131900000001, 0.087663654000000008, 0.048206815799999997, 0.094970662799999994, 0.10141340610000001, 0.1082709187, 0.085277269700000005, 0.1009383027, 0.048121372099999997, 0.033451968200000001, 0.073331336299999994, -0.021453555700000002, 0.041625241200000003, -0.050918579200000001, -0.1076689996, -0.036916995000000001, -0.087907701899999996, -0.035880144500000002, -0.067531560599999998, 0.045443701400000001, -0.020995433399999999, 0.033131181799999999, -0.024299832200000003, -0.0470639453, -0.060885063699999999, -0.058055088600000013, -0.081519278099999995, -0.080857174800000001, -0.1376300788, -0.12919356339999999, -0.064867225899999992, -0.0952414969, -0.14166033710000001, -0.054057478499999999, -0.062154847700000002, -0.1211820995, -0.1097194334, -0.1003409601, -0.026750889500000003, -0.13318793369999998], [0.0320880578, 0.13012074470000001, 0.1412351547, 0.0239499803, 0.078678664400000001, 0.011371399500000001, -0.092331951999999995, -0.034474906999999999, 0.097486598199999996, 0.1187928093, 0.0341760994, 0.019139288300000001, 0.031615493600000003, 0.0066912280000000005, -0.051102704000000006, -0.066266686200000008, -0.097852739300000005, -0.031278092200000003, -0.052582394400000003, -0.0138558104, -0.0039462630999999998, -0.092938341199999996, -0.083598689300000001, 0.023278812699999998, 0.0379015454, -0.040050381099999997, -0.097029811600000002, 0.0040087643000000003, -0.019532535, -0.026924560300000001, -0.074573407800000005, -0.021861287000000004, -0.055592252500000001, 0.016685884299999999, -0.13051911869999999, 0.094632721500000003, 0.0304729005, 0.078458453099999992, 0.013711492800000001, -0.024768567799999999, -0.062481929700000001, -0.054606966799999997, -0.098210559099999997, -0.18844416520000001, -0.069056672099999994, -0.0090246618000000001, -0.082085385900000002, -0.041483315700000002, 0.017857519700000001, 0.092331110300000005, 0.048361529600000001, 0.040752987499999997, 0.0169790093, -0.079752977599999997, -0.046840294099999999, -0.099722404599999995, -0.093294821799999997, -0.18702306639999999, -0.054664912900000001, 0.032164453199999998, 0.11523668500000001, 0.107765267, 0.013433538300000001, -0.037306069900000002, -0.0098343430000000006, -0.044155606200000003, -0.063983731099999996, 0.19781306630000001, 0.19863423120000001, 0.1124642644, 0.088739776899999998, 0.0031341709999999998, 0.0029051559999999999, 0.027395974500000003, 0.06419303400000001, 0.076901128499999999, -0.060590257000000002, -0.19378773969999999, -0.1090319617, -0.053056195700000003, -0.038201207799999998, -0.072944066500000002, -0.075156831600000001, 0.075213080500000001, 0.16961678450000001, 0.13958724089999999, 0.15102600669999999, 0.038705678200000003, -0.1216104053, -0.094228598299999994, -0.12757740480000002, 0.0969349979, -0.031276926000000004, 0.047563873600000001, 0.12814658470000001, 0.17781609550000002, 0.0391234783, 0.048983965499999997, 0.1145872622, 0.12669015559999999, 0.054037607100000003, 0.050529721900000005, 0.072776643000000002, -0.043275403600000005, 0.061133852300000013, 0.040976703599999997, -0.12028452319999999, -0.043665770399999998, -0.1101067377, 0.0128234714, -0.0071412626, 0.035723438199999999, 0.0042124175000000002, 0.086227784700000004, -0.013226508499999999, -0.027042454099999998, -0.0057705958999999998, 0.059085077999999999, -0.013786369099999999, -0.0173913108, -0.0583686229, -0.035490916300000001, 0.067940013499999993, -0.025477052100000001, -0.030548758400000001, -0.1188587201, -0.0103653685, -0.091473465300000001, -0.050732780599999999, -0.041052992400000002, 0.021231042400000004, -0.025864803400000001, -0.032849903100000001, -0.064777377999999997, -0.0296557452, -0.0127340426, 0.056237987599999997, -0.0105221133, 0.097717955600000003, -0.0766329397, -0.057162497600000001, -0.036552425299999997, -0.095863034999999999, -0.069495190900000003, -0.10769519280000001, 0.063843127200000002, 0.030614075599999999, -0.0035967124999999999, -0.013765680400000001, -0.080996548700000004, -0.0343835698, 0.0042741398999999996, -0.048751716200000003, 0.027604365200000001, 0.0017479109, 0.0056497392, -0.011714764000000001, 0.072414487200000002, -0.020521832, 0.027518121800000003, 0.024047936400000001, 0.0063981838000000003, -0.045163770800000003, 0.018078692100000002, -0.0014874802999999999, 0.018070074799999999, 0.0100305651, -0.021246006599999999, -0.0017599950000000001, -0.019624814000000001, 0.038985660999999998, -0.040806490000000001, 0.0103941382, 0.1042369207, 0.1164231901, 0.091340607599999998, 0.076977090099999992, 0.060686367599999999, -0.10734302129999999, -0.0093989581999999999], [-0.07404618360000001, -0.094020251999999999, -0.072963172199999995, -0.1677090276, -0.063856662999999994, -0.011268755199999999, -0.14657032720000002, -0.1185421913, -0.12507691769999998, -0.029922386200000001, -0.081943743999999999, 0.015444018300000001, -0.10776901699999999, 0.010149702700000001, 0.1105569762, 0.042210747700000002, 0.050000900199999997, 0.056963683000000001, 0.0065846161999999998, 0.065633760999999999, 0.021559569399999999, 0.089590400799999997, 0.092592122700000001, 0.020555357699999999, 0.030659049300000001, 0.062923456799999999, 0.088374990399999992, 0.063374199199999995, 0.10286621460000001, 0.026006781199999999, 0.1016652755, 0.12925180089999999, 0.074957513700000006, -0.042131750900000001, 0.1005681291, 0.030131305300000001, 0.012114333499999999, -0.029943607800000001, 0.043046874399999997, 0.11258079259999999, -0.027162038600000001, -0.039960323700000001, 0.1021708249, -0.013829223200000001, 0.0146285303, 0.032930977200000003, 0.059472780500000003, 0.060133871100000014, 0.0617058022, -0.035562991600000003, 0.035433294500000004, 0.083502180499999995, -0.021148279700000001, 0.091840210000000005, 0.056030184099999998, 0.1645317811, 0.027596403299999999, 0.019580386200000001, -0.1122809864, 0.0066369418000000006, -0.0286048146, -0.0082888687999999999, 0.0194031806, 0.033324777200000003, 0.0090175507999999995, 0.041418941200000003, -0.076096885500000003, -0.014511191, -0.0097917713, 0.043200582199999997, 0.024766574500000003, 0.0507621984, -0.0097589984999999994, 0.072139721599999998, 0.051247928700000001, 0.043820242300000006, -0.1127422933, -0.074076430799999995, -0.12549854939999999, -0.067960280200000001, -0.1124603158, -0.18141500520000001, -0.1181338712, -0.098977975699999998, -0.14436967539999998, 0.0440193116, 0.042738392700000002, 0.032041782799999995, -0.0111130502, -0.1196959125, -0.074692156299999993, 0.095312377399999995, -0.13304515410000001, -0.046426457599999998, -0.053157587100000001, 0.1182480025, 0.032903952400000006, 0.049336148200000006, -0.029137789899999999, 0.072144904400000001, 0.017088169600000001, -0.0415889485, 0.098540582000000002, -0.092894974800000002, -0.1096597321, -0.10471217569999999, -0.032296780800000001, -0.1157751665, -0.050322041100000006, 0.0029802428000000004, 0.043758333500000003, 0.0128351695, 0.022637819399999998, -0.0020479324999999999, 0.026853813800000001, -0.0034875167000000002, 0.0002288619, 0.036449246099999999, 0.118630833, 0.080104838600000006, 0.099757531400000002, 0.10233473849999999, 0.15028291400000002, 0.094273053400000001, 0.050110442900000003, -0.1073879309, -0.089689196799999996, -0.048190511900000003, 0.046369176200000001, 0.045138616300000003, 0.076167955699999998, 0.07360490900000001, 0.028702656300000001, -0.018917997200000002, -0.080417005599999994, -0.015529982499999999, -0.15812108120000001, 0.0229495041, 0.1123836227, -0.076133992900000003, -0.13957697569999999, -0.13450262630000001, -0.080284240000000007, -0.048899282199999998, -0.0331885081, -0.039820128500000003, -0.018381057100000001, 0.066083501900000008, 0.0153182944, -0.0189205741, 0.0395984962, 0.029206376700000002, 0.078240349900000006, -0.075634219799999999, -0.034911722100000001, 0.0228787217, 0.069368218799999992, -0.0156508016, -0.0075922398, -0.0202444073, -0.023300752200000004, 0.0168287531, 0.077331469400000005, 0.056664653200000012, 0.063451734999999995, -0.024576799699999999, -0.016257608999999999, -0.043999974900000002, -0.099474367600000002, -0.032843924699999999, -0.1119562673, -0.1088102588, -0.036089787999999998, -0.061994486799999998, 0.042538110400000002, 0.054300848200000001, 0.071870227300000006, 0.13802269810000001, 0.091616283500000006, 0.058382107900000001]])]
time_repetition = 2.5
In [98]:
finger_cond = ['Finger','T', ['Finger'],[1]]
foot_cond = ['Foot','T', ['Foot'],[1]]
lips_cond = ['Lips','T', ['Lips'],[1]]
lips_vs_others = ["Lips vs. others",'T', ['Finger', 'Foot', 'Lips'],[-0.5, -0.5, 1]]
all_motor = ["All motor", 'F', [finger_cond, foot_cond, lips_cond]]
contrasts=[finger_cond, foot_cond, lips_cond, lips_vs_others, all_motor]
level1design = mem.cache(fsl.model.Level1Design)
level1design_results = level1design(interscan_interval = layout.get_metadata(source_epi.filename)["RepetitionTime"],
bases = {'dgamma':{'derivs': True}},
session_info = specify_model_results.outputs.session_info,
model_serial_correlations=True,
contrasts=contrasts)
level1design_results.outputs
170216-19:47:45,544 workflow INFO:
Executing node 74d7ae2936d9ccca52dab5eb907b61fa in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa
170216-19:47:45,558 workflow INFO:
Collecting precomputed outputs
Out[98]:
ev_files = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_Finger_0_1.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_Foot_0_3.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_Lips_0_5.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_FramewiseDisplacement_0_7.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor0_0_8.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor1_0_9.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor2_0_10.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor3_0_11.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor4_0_12.txt', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/ev_aCompCor5_0_13.txt']
fsf_files = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa/run0.fsf
In [99]:
modelgen = mem.cache(fsl.model.FEATModel)
modelgen_results = modelgen(fsf_file=level1design_results.outputs.fsf_files,
ev_files=level1design_results.outputs.ev_files)
modelgen_results.outputs
170216-19:47:46,674 workflow INFO:
Executing node 8945ac8cd548642ea78bb3a88c03794e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e
170216-19:47:46,678 workflow INFO:
Collecting precomputed outputs
Out[99]:
con_file = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e/run0.con
design_cov = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e/run0_cov.png
design_file = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e/run0.mat
design_image = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e/run0.png
fcon_file = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e/run0.fts
In [100]:
desmtx=numpy.loadtxt(modelgen_results.outputs.design_file,skiprows=5)
plt.imshow(desmtx,aspect='auto',interpolation='nearest',cmap='gray')
Out[100]:
<matplotlib.image.AxesImage at 0x7f2dbf59a550>
In [101]:
cc=numpy.corrcoef(desmtx.T)
plt.imshow(cc,aspect='auto',interpolation='nearest', cmap=plt.cm.viridis)
plt.colorbar()
Out[101]:
<matplotlib.colorbar.Colorbar at 0x7f2db47ad2e8>
In [102]:
mask = mem.cache(fsl.maths.ApplyMask)
mask_results = mask(in_file=skip_results.outputs.roi_file,
mask_file=os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz"%(source_epi.subject,
source_epi.session)))
mask_results.outputs
170216-19:47:49,936 workflow INFO:
Executing node 6d5befc3d283e8805d34e8668614b457 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/6d5befc3d283e8805d34e8668614b457
170216-19:47:49,944 workflow INFO:
Collecting precomputed outputs
Out[102]:
out_file = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/6d5befc3d283e8805d34e8668614b457/sub-06_ses-test_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_preproc_roi_masked.nii.gz
In [103]:
filmgls= mem.cache(fsl.FILMGLS)
filmgls_results = filmgls(in_file=mask_results.outputs.out_file,
design_file = modelgen_results.outputs.design_file,
tcon_file = modelgen_results.outputs.con_file,
fcon_file = modelgen_results.outputs.fcon_file,
autocorr_noestimate = True)
filmgls_results.outputs
170216-19:47:51,7 workflow INFO:
Executing node 7f5c5f51c2e4db65146003eb9b361a34 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34
170216-19:47:51,10 workflow INFO:
Collecting precomputed outputs
Out[103]:
copes = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/cope1.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/cope2.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/cope3.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/cope4.nii.gz']
dof_file = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/dof
fstats = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/fstat1.nii.gz
logfile = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/logfile
param_estimates = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe1.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe2.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe3.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe4.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe5.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe6.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe7.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe8.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe9.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe10.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe11.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe12.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/pe13.nii.gz']
residual4d = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/res4d.nii.gz
results_dir = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results
sigmasquareds = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/sigmasquareds.nii.gz
thresholdac = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/threshac1.nii.gz
tstats = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/tstat1.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/tstat2.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/tstat3.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/tstat4.nii.gz']
varcopes = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/varcope1.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/varcope2.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/varcope3.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/varcope4.nii.gz']
zfstats = /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/zfstat1.nii.gz
zstats = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/zstat1.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/zstat2.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/zstat3.nii.gz', '/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34/results/zstat4.nii.gz']
In [104]:
for t_map in filmgls_results.outputs.zstats:
nilearn.plotting.plot_glass_brain(nilearn.image.smooth_img(t_map, 8),
display_mode='lyrz', colorbar=True, plot_abs=False, threshold=2.3)
In [105]:
for t_map in [filmgls_results.outputs.zfstats]:
nilearn.plotting.plot_glass_brain(nilearn.image.smooth_img(t_map, 8),
display_mode='lyrz', colorbar=True, plot_abs=False, threshold=2.3)
In [106]:
for t_map in filmgls_results.outputs.copes:
nilearn.plotting.plot_glass_brain(nilearn.image.smooth_img(t_map, 8),
display_mode='lyrz', colorbar=True, plot_abs=False, vmax=30)
In [107]:
for t_map in filmgls_results.outputs.tstats:
nilearn.plotting.plot_stat_map(nilearn.image.smooth_img(t_map, 8), colorbar=True, threshold=2.3)
For the group level analysis we need to move results from all subjects into one common MNI space. Let's start with the EPI derived mask (we will use it later for group level mask)
In [109]:
copes = {}
for i in range(10):
source_epi = layout.get(type="bold", task="fingerfootlips", session="test", extensions="nii.gz")[i]
confounds = pd.read_csv(os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_confounds.tsv"%(source_epi.subject,
source_epi.session)),
sep="\t", na_values="n/a")
info = [Bunch(conditions=['Finger',
'Foot',
'Lips'],
onsets=[list(events[events.trial_type == 'Finger'].onset-10),
list(events[events.trial_type == 'Foot'].onset-10),
list(events[events.trial_type == 'Lips'].onset-10)],
durations=[list(events[events.trial_type == 'Finger'].duration),
list(events[events.trial_type == 'Foot'].duration),
list(events[events.trial_type == 'Lips'].duration)],
regressors=[list(confounds.FramewiseDisplacement.fillna(0)[4:]),
list(confounds.aCompCor0[4:]),
list(confounds.aCompCor1[4:]),
list(confounds.aCompCor2[4:]),
list(confounds.aCompCor3[4:]),
list(confounds.aCompCor4[4:]),
list(confounds.aCompCor5[4:]),
],
regressor_names=['FramewiseDisplacement',
'aCompCor0',
'aCompCor1',
'aCompCor2',
'aCompCor3',
'aCompCor4',
'aCompCor5',])
]
skip = mem.cache(fsl.ExtractROI)
skip_results = skip(in_file=os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_preproc.nii.gz"%(source_epi.subject,
source_epi.session)),
t_min=4, t_size=-1)
s = model.SpecifyModel()
s.inputs.input_units = 'secs'
s.inputs.functional_runs = skip_results.outputs.roi_file
s.inputs.time_repetition = layout.get_metadata(source_epi.filename)["RepetitionTime"]
s.inputs.high_pass_filter_cutoff = 128.
s.inputs.subject_info = info
specify_model_results = s.run()
finger_cond = ['Finger','T', ['Finger'],[1]]
foot_cond = ['Foot','T', ['Foot'],[1]]
lips_cond = ['Lips','T', ['Lips'],[1]]
lips_vs_others = ["Lips vs. others",'T', ['Finger', 'Foot', 'Lips'],[-0.5, -0.5, 1]]
all_motor = ["All motor", 'F', [finger_cond, foot_cond, lips_cond]]
contrasts=[finger_cond, foot_cond, lips_cond, lips_vs_others, all_motor]
level1design = mem.cache(fsl.model.Level1Design)
level1design_results = level1design(interscan_interval = layout.get_metadata(source_epi.filename)["RepetitionTime"],
bases = {'dgamma':{'derivs': True}},
session_info = specify_model_results.outputs.session_info,
model_serial_correlations=True,
contrasts=contrasts)
modelgen = mem.cache(fsl.model.FEATModel)
modelgen_results = modelgen(fsf_file=level1design_results.outputs.fsf_files,
ev_files=level1design_results.outputs.ev_files)
mask = mem.cache(fsl.maths.ApplyMask)
mask_results = mask(in_file=skip_results.outputs.roi_file,
mask_file=os.path.join(datadir, "derivatives", "fmriprep",
"sub-%s"%source_epi.subject, "ses-%s"%source_epi.session, "func",
"sub-%s_ses-%s_task-fingerfootlips_bold_space-MNI152NLin2009cAsym_brainmask.nii.gz"%(source_epi.subject,
source_epi.session)))
filmgls= mem.cache(fsl.FILMGLS)
filmgls_results = filmgls(in_file=mask_results.outputs.out_file,
design_file = modelgen_results.outputs.design_file,
tcon_file = modelgen_results.outputs.con_file,
fcon_file = modelgen_results.outputs.fcon_file,
autocorr_noestimate = True)
copes[source_epi.subject] = list(filmgls_results.outputs.copes)
170216-19:48:19,965 workflow INFO:
Executing node 174cdf719080398538e308387b24f09e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/174cdf719080398538e308387b24f09e
170216-19:48:19,970 workflow INFO:
Collecting precomputed outputs
170216-19:48:19,996 workflow INFO:
Executing node a386190248c0e00d040c4f2acace5e81 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/a386190248c0e00d040c4f2acace5e81
170216-19:48:20,11 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,19 workflow INFO:
Executing node 1edff29b476cd009678abc7a05af37ad in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/1edff29b476cd009678abc7a05af37ad
170216-19:48:20,20 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,35 workflow INFO:
Executing node 9874639b92a90656f4d4da94d3cd4fbd in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/9874639b92a90656f4d4da94d3cd4fbd
170216-19:48:20,41 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,48 workflow INFO:
Executing node c040260ebf80a99fd6f7c94e5ec62642 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/c040260ebf80a99fd6f7c94e5ec62642
170216-19:48:20,51 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,110 workflow INFO:
Executing node df5cf35d0841dfd6159bd543c0726a19 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/df5cf35d0841dfd6159bd543c0726a19
170216-19:48:20,120 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,154 workflow INFO:
Executing node 663e41cd0ce32167cf6bc952b9aa2897 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/663e41cd0ce32167cf6bc952b9aa2897
170216-19:48:20,171 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,180 workflow INFO:
Executing node d1f1110ceeee74b68aa55cc8a8752cf2 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/d1f1110ceeee74b68aa55cc8a8752cf2
170216-19:48:20,183 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,206 workflow INFO:
Executing node 7a2bf8d1a6ff37a22da525a7862df1ec in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/7a2bf8d1a6ff37a22da525a7862df1ec
170216-19:48:20,212 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,224 workflow INFO:
Executing node 847007f9fc325323aaa555f39243dc46 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/847007f9fc325323aaa555f39243dc46
170216-19:48:20,226 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,280 workflow INFO:
Executing node a87e39e5ea228ccea321624351653327 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/a87e39e5ea228ccea321624351653327
170216-19:48:20,286 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,316 workflow INFO:
Executing node 2f1518bf459acf0cc6ce10183b5a27be in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/2f1518bf459acf0cc6ce10183b5a27be
170216-19:48:20,329 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,337 workflow INFO:
Executing node dfe48257b9f9611f0ece1e2d8d3c212d in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/dfe48257b9f9611f0ece1e2d8d3c212d
170216-19:48:20,339 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,351 workflow INFO:
Executing node 18587b67f8968fc237628ca37c3bfd9e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/18587b67f8968fc237628ca37c3bfd9e
170216-19:48:20,357 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,369 workflow INFO:
Executing node 5207f88ce27cefc8201d33ad7e328adf in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/5207f88ce27cefc8201d33ad7e328adf
170216-19:48:20,373 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,414 workflow INFO:
Executing node f082170025d44f3f272d44be2bae6cda in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/f082170025d44f3f272d44be2bae6cda
170216-19:48:20,420 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,450 workflow INFO:
Executing node 4c1a1589ef0f6fa4e994bbb3cceaaa16 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/4c1a1589ef0f6fa4e994bbb3cceaaa16
170216-19:48:20,468 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,475 workflow INFO:
Executing node 5948f382f97cc48fc89922d367352bf1 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/5948f382f97cc48fc89922d367352bf1
170216-19:48:20,477 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,490 workflow INFO:
Executing node 312515eead0b6495671320846adbc6ec in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/312515eead0b6495671320846adbc6ec
170216-19:48:20,495 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,504 workflow INFO:
Executing node ad4af5b0f670ab40ca38d962a8464b76 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/ad4af5b0f670ab40ca38d962a8464b76
170216-19:48:20,506 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,543 workflow INFO:
Executing node 0bf27e5d88804cb43b9db39240f2d6a2 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/0bf27e5d88804cb43b9db39240f2d6a2
170216-19:48:20,547 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,577 workflow INFO:
Executing node 18e09bab7f60ab06e1b530fa9150b1cf in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/18e09bab7f60ab06e1b530fa9150b1cf
170216-19:48:20,589 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,595 workflow INFO:
Executing node 7838507a3c4afc259e90a0d8796f5fdc in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/7838507a3c4afc259e90a0d8796f5fdc
170216-19:48:20,597 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,608 workflow INFO:
Executing node 0dab1f768d5f6572126ed4368cb3719e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/0dab1f768d5f6572126ed4368cb3719e
170216-19:48:20,612 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,620 workflow INFO:
Executing node 39aa691cfbc8be2a3a7be06c268b317e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/39aa691cfbc8be2a3a7be06c268b317e
170216-19:48:20,622 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,672 workflow INFO:
Executing node 2173ff0bacc206ded70e35bfa7c6900d in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/2173ff0bacc206ded70e35bfa7c6900d
170216-19:48:20,678 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,708 workflow INFO:
Executing node 74d7ae2936d9ccca52dab5eb907b61fa in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/74d7ae2936d9ccca52dab5eb907b61fa
170216-19:48:20,722 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,728 workflow INFO:
Executing node 8945ac8cd548642ea78bb3a88c03794e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8945ac8cd548642ea78bb3a88c03794e
170216-19:48:20,730 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,742 workflow INFO:
Executing node 6d5befc3d283e8805d34e8668614b457 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/6d5befc3d283e8805d34e8668614b457
170216-19:48:20,747 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,756 workflow INFO:
Executing node 7f5c5f51c2e4db65146003eb9b361a34 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7f5c5f51c2e4db65146003eb9b361a34
170216-19:48:20,760 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,797 workflow INFO:
Executing node 944821bfdcf02f9d3efea7873688d6fa in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/944821bfdcf02f9d3efea7873688d6fa
170216-19:48:20,803 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,831 workflow INFO:
Executing node fc1b3b8c413725293f46b2a53e8498b9 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/fc1b3b8c413725293f46b2a53e8498b9
170216-19:48:20,845 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,853 workflow INFO:
Executing node ee3261b722622a05e8765bdfc032c36e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/ee3261b722622a05e8765bdfc032c36e
170216-19:48:20,854 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,864 workflow INFO:
Executing node 65d5eeec8095591fb2efb3143e00794d in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/65d5eeec8095591fb2efb3143e00794d
170216-19:48:20,869 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,879 workflow INFO:
Executing node 26f885b83dded93816ed430bf1fa7fe3 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/26f885b83dded93816ed430bf1fa7fe3
170216-19:48:20,881 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,916 workflow INFO:
Executing node 78e714b69e8859aa74b489f1c679b9a2 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/78e714b69e8859aa74b489f1c679b9a2
170216-19:48:20,924 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,954 workflow INFO:
Executing node 45894ce0af230a80195cedf44a12e44a in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/45894ce0af230a80195cedf44a12e44a
170216-19:48:20,969 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,977 workflow INFO:
Executing node 8e6be4cc03eadac42941652c8db4ec30 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/8e6be4cc03eadac42941652c8db4ec30
170216-19:48:20,980 workflow INFO:
Collecting precomputed outputs
170216-19:48:20,991 workflow INFO:
Executing node 11398bca492232227201080d5e4dd78e in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/11398bca492232227201080d5e4dd78e
170216-19:48:20,998 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,7 workflow INFO:
Executing node 9e68ad2352f795dbd124ba56046a72ce in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/9e68ad2352f795dbd124ba56046a72ce
170216-19:48:21,12 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,54 workflow INFO:
Executing node 28bd985b6d25fd026c4a00e0fc478cdc in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/28bd985b6d25fd026c4a00e0fc478cdc
170216-19:48:21,59 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,89 workflow INFO:
Executing node 1fffdcd888ede5d8fc07bf96cc7a8082 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/1fffdcd888ede5d8fc07bf96cc7a8082
170216-19:48:21,105 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,113 workflow INFO:
Executing node 883619cf93e295a142c4c53ae1efd643 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/883619cf93e295a142c4c53ae1efd643
170216-19:48:21,116 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,134 workflow INFO:
Executing node 77d2a920c28ca30a4ef49bfb79227b1f in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/77d2a920c28ca30a4ef49bfb79227b1f
170216-19:48:21,142 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,153 workflow INFO:
Executing node f67a843ef2920b1171320d8718e9c378 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/f67a843ef2920b1171320d8718e9c378
170216-19:48:21,156 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,205 workflow INFO:
Executing node 740d95b5b23a28bfa73b979ba0847aad in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-utils-ExtractROI/740d95b5b23a28bfa73b979ba0847aad
170216-19:48:21,217 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,275 workflow INFO:
Executing node a3ac36a9e3c9ea4d1e6ab7bbabb3396b in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Level1Design/a3ac36a9e3c9ea4d1e6ab7bbabb3396b
170216-19:48:21,297 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,307 workflow INFO:
Executing node 378fb6f988e63c5e2a3bb7b64ec5a592 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FEATModel/378fb6f988e63c5e2a3bb7b64ec5a592
170216-19:48:21,309 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,341 workflow INFO:
Executing node edec0e04e83edf247d2b53bbce3348e5 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-maths-ApplyMask/edec0e04e83edf247d2b53bbce3348e5
170216-19:48:21,354 workflow INFO:
Collecting precomputed outputs
170216-19:48:21,366 workflow INFO:
Executing node 7b8821caf74eba38eacdf8874e1370a5 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-FILMGLS/7b8821caf74eba38eacdf8874e1370a5
170216-19:48:21,370 workflow INFO:
Collecting precomputed outputs
In [110]:
smooth_copes = []
for k,v in copes.items():
smooth_cope = nilearn.image.smooth_img(v[3], 8)
smooth_copes.append(smooth_cope)
nilearn.plotting.plot_glass_brain(smooth_cope,
display_mode='lyrz',
colorbar=True,
plot_abs=False,
vmax=30)
In [111]:
nilearn.plotting.plot_glass_brain(nilearn.image.mean_img(smooth_copes),
display_mode='lyrz',
colorbar=True,
plot_abs=False)
Out[111]:
<nilearn.plotting.displays.LYRZProjector at 0x7f2dafaf86d8>
In [112]:
brainmasks = glob.glob(os.path.join(datadir, "derivatives", "fmriprep", "sub-*", "ses-test", "func", "*task-fingerfootlips_*space-MNI152NLin2009cAsym*_brainmask.nii*"))
for mask in brainmasks:
nilearn.plotting.plot_roi(mask)
mean_mask = nilearn.image.mean_img(brainmasks)
nilearn.plotting.plot_stat_map(mean_mask)
group_mask = nilearn.image.math_img("a>=0.95", a=mean_mask)
nilearn.plotting.plot_roi(group_mask)
Out[112]:
<nilearn.plotting.displays.OrthoSlicer at 0x7f2dc08ca9e8>
In [113]:
!mkdir -p {datadir}/derivatives/custom_modelling/
copes_concat = nilearn.image.concat_imgs(smooth_copes, auto_resample=True)
copes_concat.to_filename(os.path.join(datadir, "derivatives", "custom_modelling", "lips_vs_others_copes.nii.gz"))
group_mask = nilearn.image.resample_to_img(group_mask, copes_concat, interpolation='nearest')
group_mask.to_filename(os.path.join(datadir, "derivatives", "custom_modelling", "group_mask.nii.gz"))
/home/vagrant/miniconda3/lib/python3.5/site-packages/nilearn/_utils/niimg_conversions.py:144: UserWarning: Affine is different across subjects. Realignement on first subject affine forced
warnings.warn('Affine is different across subjects.'
In [114]:
group_mask.shape
Out[114]:
(49, 58, 49)
In [115]:
randomise = mem.cache(fsl.Randomise)
randomise_results = randomise(in_file=os.path.join(datadir, "derivatives", "custom_modelling", "lips_vs_others_copes.nii.gz"),
mask=os.path.join(datadir, "derivatives", "custom_modelling", "group_mask.nii.gz"),
one_sample_group_mean=True,
tfce=True,
vox_p_values=True,
num_perm=500)
randomise_results.outputs
170216-19:49:12,516 workflow INFO:
Executing node 393fecf255fa7f15245cd7fa32e0d3c0 in dir: /home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Randomise/393fecf255fa7f15245cd7fa32e0d3c0
170216-19:49:12,534 workflow INFO:
Running: randomise -i /media/sf_ds000114_R2.0.1/derivatives/custom_modelling/lips_vs_others_copes.nii.gz -o "tbss_" -m /media/sf_ds000114_R2.0.1/derivatives/custom_modelling/group_mask.nii.gz -n 500 -1 -T -x
170216-19:49:12,585 interface INFO:
stdout 2017-02-16T19:49:12.585130:randomise options: -i /media/sf_ds000114_R2.0.1/derivatives/custom_modelling/lips_vs_others_copes.nii.gz -o tbss_ -m /media/sf_ds000114_R2.0.1/derivatives/custom_modelling/group_mask.nii.gz -n 500 -1 -T -x
170216-19:49:13,89 interface INFO:
stdout 2017-02-16T19:49:13.089743:Loading Data:
170216-19:49:13,90 interface INFO:
stdout 2017-02-16T19:49:13.089743:Data loaded
170216-19:49:13,95 interface INFO:
stdout 2017-02-16T19:49:13.089743:One-sample design detected; sign-flipping instead of permuting.
170216-19:49:13,106 interface INFO:
stdout 2017-02-16T19:49:13.089743:1024 sign-flips required for exhaustive test of t-test 1
170216-19:49:13,107 interface INFO:
stdout 2017-02-16T19:49:13.089743:Doing 500 random permutations
170216-19:49:13,109 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 1 (Unpermuted data)
170216-19:49:13,110 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 2
170216-19:49:13,112 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 3
170216-19:49:13,118 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 4
170216-19:49:13,120 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 5
170216-19:49:13,122 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 6
170216-19:49:13,130 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 7
170216-19:49:13,132 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 8
170216-19:49:13,133 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 9
170216-19:49:13,134 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 10
170216-19:49:13,143 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 11
170216-19:49:13,144 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 12
170216-19:49:13,145 interface INFO:
stdout 2017-02-16T19:49:13.089743:Starting permutation 13
170216-19:49:13,656 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 14
170216-19:49:13,656 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 15
170216-19:49:13,658 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 16
170216-19:49:13,659 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 17
170216-19:49:13,666 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 18
170216-19:49:13,667 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 19
170216-19:49:13,668 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 20
170216-19:49:13,670 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 21
170216-19:49:13,682 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 22
170216-19:49:13,684 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 23
170216-19:49:13,686 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 24
170216-19:49:13,688 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 25
170216-19:49:13,689 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 26
170216-19:49:13,699 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 27
170216-19:49:13,700 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 28
170216-19:49:13,701 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 29
170216-19:49:13,702 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 30
170216-19:49:13,704 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 31
170216-19:49:13,714 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 32
170216-19:49:13,716 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 33
170216-19:49:13,717 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 34
170216-19:49:13,718 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 35
170216-19:49:13,719 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 36
170216-19:49:13,720 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 37
170216-19:49:13,730 interface INFO:
stdout 2017-02-16T19:49:13.655931:Starting permutation 38
170216-19:49:14,232 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 39
170216-19:49:14,233 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 40
170216-19:49:14,247 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 41
170216-19:49:14,249 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 42
170216-19:49:14,250 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 43
170216-19:49:14,262 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 44
170216-19:49:14,264 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 45
170216-19:49:14,265 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 46
170216-19:49:14,266 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 47
170216-19:49:14,267 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 48
170216-19:49:14,268 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 49
170216-19:49:14,269 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 50
170216-19:49:14,272 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 51
170216-19:49:14,278 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 52
170216-19:49:14,279 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 53
170216-19:49:14,290 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 54
170216-19:49:14,291 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 55
170216-19:49:14,292 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 56
170216-19:49:14,293 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 57
170216-19:49:14,294 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 58
170216-19:49:14,295 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 59
170216-19:49:14,297 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 60
170216-19:49:14,304 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 61
170216-19:49:14,305 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 62
170216-19:49:14,306 interface INFO:
stdout 2017-02-16T19:49:14.232861:Starting permutation 63
170216-19:49:14,808 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 64
170216-19:49:14,808 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 65
170216-19:49:14,812 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 66
170216-19:49:14,813 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 67
170216-19:49:14,826 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 68
170216-19:49:14,827 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 69
170216-19:49:14,828 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 70
170216-19:49:14,829 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 71
170216-19:49:14,831 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 72
170216-19:49:14,832 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 73
170216-19:49:14,833 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 74
170216-19:49:14,834 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 75
170216-19:49:14,836 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 76
170216-19:49:14,846 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 77
170216-19:49:14,847 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 78
170216-19:49:14,849 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 79
170216-19:49:14,851 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 80
170216-19:49:14,852 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 81
170216-19:49:14,853 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 82
170216-19:49:14,854 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 83
170216-19:49:14,865 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 84
170216-19:49:14,866 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 85
170216-19:49:14,867 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 86
170216-19:49:14,868 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 87
170216-19:49:14,869 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 88
170216-19:49:14,870 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 89
170216-19:49:14,871 interface INFO:
stdout 2017-02-16T19:49:14.807985:Starting permutation 90
170216-19:49:15,374 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 91
170216-19:49:15,375 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 92
170216-19:49:15,377 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 93
170216-19:49:15,378 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 94
170216-19:49:15,379 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 95
170216-19:49:15,387 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 96
170216-19:49:15,388 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 97
170216-19:49:15,389 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 98
170216-19:49:15,390 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 99
170216-19:49:15,391 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 100
170216-19:49:15,392 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 101
170216-19:49:15,398 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 102
170216-19:49:15,399 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 103
170216-19:49:15,401 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 104
170216-19:49:15,410 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 105
170216-19:49:15,412 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 106
170216-19:49:15,413 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 107
170216-19:49:15,414 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 108
170216-19:49:15,415 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 109
170216-19:49:15,423 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 110
170216-19:49:15,424 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 111
170216-19:49:15,425 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 112
170216-19:49:15,427 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 113
170216-19:49:15,432 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 114
170216-19:49:15,433 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 115
170216-19:49:15,447 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 116
170216-19:49:15,448 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 117
170216-19:49:15,449 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 118
170216-19:49:15,450 interface INFO:
stdout 2017-02-16T19:49:15.374630:Starting permutation 119
170216-19:49:15,952 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 120
170216-19:49:15,953 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 121
170216-19:49:15,954 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 122
170216-19:49:15,955 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 123
170216-19:49:15,956 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 124
170216-19:49:15,957 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 125
170216-19:49:15,964 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 126
170216-19:49:15,966 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 127
170216-19:49:15,967 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 128
170216-19:49:15,968 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 129
170216-19:49:15,969 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 130
170216-19:49:15,978 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 131
170216-19:49:15,979 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 132
170216-19:49:15,981 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 133
170216-19:49:15,983 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 134
170216-19:49:15,984 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 135
170216-19:49:15,985 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 136
170216-19:49:15,991 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 137
170216-19:49:15,992 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 138
170216-19:49:15,993 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 139
170216-19:49:15,998 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 140
170216-19:49:16,0 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 141
170216-19:49:16,10 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 142
170216-19:49:16,12 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 143
170216-19:49:16,14 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 144
170216-19:49:16,27 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 145
170216-19:49:16,28 interface INFO:
stdout 2017-02-16T19:49:15.952485:Starting permutation 146
170216-19:49:16,530 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 147
170216-19:49:16,532 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 148
170216-19:49:16,533 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 149
170216-19:49:16,534 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 150
170216-19:49:16,546 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 151
170216-19:49:16,548 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 152
170216-19:49:16,549 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 153
170216-19:49:16,550 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 154
170216-19:49:16,551 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 155
170216-19:49:16,552 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 156
170216-19:49:16,553 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 157
170216-19:49:16,554 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 158
170216-19:49:16,555 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 159
170216-19:49:16,565 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 160
170216-19:49:16,566 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 161
170216-19:49:16,568 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 162
170216-19:49:16,569 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 163
170216-19:49:16,570 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 164
170216-19:49:16,582 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 165
170216-19:49:16,583 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 166
170216-19:49:16,584 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 167
170216-19:49:16,585 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 168
170216-19:49:16,586 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 169
170216-19:49:16,587 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 170
170216-19:49:16,588 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 171
170216-19:49:16,599 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 172
170216-19:49:16,600 interface INFO:
stdout 2017-02-16T19:49:16.530356:Starting permutation 173
170216-19:49:17,102 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 174
170216-19:49:17,103 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 175
170216-19:49:17,104 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 176
170216-19:49:17,105 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 177
170216-19:49:17,106 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 178
170216-19:49:17,107 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 179
170216-19:49:17,115 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 180
170216-19:49:17,116 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 181
170216-19:49:17,117 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 182
170216-19:49:17,118 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 183
170216-19:49:17,119 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 184
170216-19:49:17,130 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 185
170216-19:49:17,131 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 186
170216-19:49:17,133 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 187
170216-19:49:17,134 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 188
170216-19:49:17,135 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 189
170216-19:49:17,136 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 190
170216-19:49:17,146 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 191
170216-19:49:17,147 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 192
170216-19:49:17,149 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 193
170216-19:49:17,151 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 194
170216-19:49:17,152 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 195
170216-19:49:17,163 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 196
170216-19:49:17,164 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 197
170216-19:49:17,166 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 198
170216-19:49:17,166 interface INFO:
stdout 2017-02-16T19:49:17.102237:Starting permutation 199
170216-19:49:17,668 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 200
170216-19:49:17,669 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 201
170216-19:49:17,670 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 202
170216-19:49:17,672 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 203
170216-19:49:17,673 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 204
170216-19:49:17,674 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 205
170216-19:49:17,681 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 206
170216-19:49:17,683 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 207
170216-19:49:17,685 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 208
170216-19:49:17,694 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 209
170216-19:49:17,695 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 210
170216-19:49:17,697 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 211
170216-19:49:17,699 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 212
170216-19:49:17,701 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 213
170216-19:49:17,703 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 214
170216-19:49:17,705 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 215
170216-19:49:17,714 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 216
170216-19:49:17,716 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 217
170216-19:49:17,718 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 218
170216-19:49:17,720 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 219
170216-19:49:17,722 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 220
170216-19:49:17,733 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 221
170216-19:49:17,734 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 222
170216-19:49:17,735 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 223
170216-19:49:17,736 interface INFO:
stdout 2017-02-16T19:49:17.668546:Starting permutation 224
170216-19:49:18,240 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 225
170216-19:49:18,240 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 226
170216-19:49:18,243 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 227
170216-19:49:18,244 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 228
170216-19:49:18,245 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 229
170216-19:49:18,258 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 230
170216-19:49:18,259 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 231
170216-19:49:18,260 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 232
170216-19:49:18,261 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 233
170216-19:49:18,262 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 234
170216-19:49:18,263 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 235
170216-19:49:18,265 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 236
170216-19:49:18,267 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 237
170216-19:49:18,278 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 238
170216-19:49:18,280 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 239
170216-19:49:18,281 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 240
170216-19:49:18,283 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 241
170216-19:49:18,284 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 242
170216-19:49:18,285 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 243
170216-19:49:18,294 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 244
170216-19:49:18,296 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 245
170216-19:49:18,297 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 246
170216-19:49:18,298 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 247
170216-19:49:18,299 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 248
170216-19:49:18,301 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 249
170216-19:49:18,310 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 250
170216-19:49:18,311 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 251
170216-19:49:18,313 interface INFO:
stdout 2017-02-16T19:49:18.239932:Starting permutation 252
170216-19:49:18,815 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 253
170216-19:49:18,817 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 254
170216-19:49:18,818 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 255
170216-19:49:18,820 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 256
170216-19:49:18,830 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 257
170216-19:49:18,831 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 258
170216-19:49:18,833 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 259
170216-19:49:18,834 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 260
170216-19:49:18,835 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 261
170216-19:49:18,846 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 262
170216-19:49:18,847 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 263
170216-19:49:18,849 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 264
170216-19:49:18,850 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 265
170216-19:49:18,852 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 266
170216-19:49:18,853 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 267
170216-19:49:18,854 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 268
170216-19:49:18,865 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 269
170216-19:49:18,867 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 270
170216-19:49:18,868 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 271
170216-19:49:18,869 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 272
170216-19:49:18,870 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 273
170216-19:49:18,871 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 274
170216-19:49:18,881 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 275
170216-19:49:18,882 interface INFO:
stdout 2017-02-16T19:49:18.815795:Starting permutation 276
170216-19:49:19,384 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 277
170216-19:49:19,386 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 278
170216-19:49:19,387 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 279
170216-19:49:19,388 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 280
170216-19:49:19,398 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 281
170216-19:49:19,400 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 282
170216-19:49:19,401 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 283
170216-19:49:19,402 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 284
170216-19:49:19,403 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 285
170216-19:49:19,404 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 286
170216-19:49:19,405 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 287
170216-19:49:19,421 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 288
170216-19:49:19,422 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 289
170216-19:49:19,422 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 290
170216-19:49:19,423 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 291
170216-19:49:19,424 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 292
170216-19:49:19,425 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 293
170216-19:49:19,425 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 294
170216-19:49:19,426 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 295
170216-19:49:19,426 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 296
170216-19:49:19,427 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 297
170216-19:49:19,427 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 298
170216-19:49:19,429 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 299
170216-19:49:19,430 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 300
170216-19:49:19,430 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 301
170216-19:49:19,434 interface INFO:
stdout 2017-02-16T19:49:19.384490:Starting permutation 302
170216-19:49:19,937 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 303
170216-19:49:19,937 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 304
170216-19:49:19,938 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 305
170216-19:49:19,938 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 306
170216-19:49:19,939 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 307
170216-19:49:19,939 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 308
170216-19:49:19,940 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 309
170216-19:49:19,941 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 310
170216-19:49:19,941 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 311
170216-19:49:19,942 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 312
170216-19:49:19,942 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 313
170216-19:49:19,943 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 314
170216-19:49:19,943 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 315
170216-19:49:19,943 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 316
170216-19:49:19,944 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 317
170216-19:49:19,944 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 318
170216-19:49:19,945 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 319
170216-19:49:19,948 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 320
170216-19:49:19,949 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 321
170216-19:49:19,953 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 322
170216-19:49:19,954 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 323
170216-19:49:19,954 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 324
170216-19:49:19,955 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 325
170216-19:49:19,955 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 326
170216-19:49:19,956 interface INFO:
stdout 2017-02-16T19:49:19.937021:Starting permutation 327
170216-19:49:20,457 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 328
170216-19:49:20,458 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 329
170216-19:49:20,458 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 330
170216-19:49:20,459 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 331
170216-19:49:20,459 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 332
170216-19:49:20,460 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 333
170216-19:49:20,460 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 334
170216-19:49:20,461 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 335
170216-19:49:20,461 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 336
170216-19:49:20,462 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 337
170216-19:49:20,462 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 338
170216-19:49:20,463 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 339
170216-19:49:20,463 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 340
170216-19:49:20,464 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 341
170216-19:49:20,465 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 342
170216-19:49:20,467 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 343
170216-19:49:20,470 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 344
170216-19:49:20,471 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 345
170216-19:49:20,471 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 346
170216-19:49:20,472 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 347
170216-19:49:20,472 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 348
170216-19:49:20,473 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 349
170216-19:49:20,473 interface INFO:
stdout 2017-02-16T19:49:20.457459:Starting permutation 350
170216-19:49:20,974 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 351
170216-19:49:20,975 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 352
170216-19:49:20,976 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 353
170216-19:49:20,977 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 354
170216-19:49:20,977 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 355
170216-19:49:20,978 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 356
170216-19:49:20,978 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 357
170216-19:49:20,979 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 358
170216-19:49:20,980 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 359
170216-19:49:20,980 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 360
170216-19:49:20,981 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 361
170216-19:49:20,982 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 362
170216-19:49:20,983 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 363
170216-19:49:20,983 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 364
170216-19:49:20,984 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 365
170216-19:49:20,986 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 366
170216-19:49:20,986 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 367
170216-19:49:20,991 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 368
170216-19:49:20,992 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 369
170216-19:49:20,993 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 370
170216-19:49:20,994 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 371
170216-19:49:20,994 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 372
170216-19:49:20,995 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 373
170216-19:49:20,995 interface INFO:
stdout 2017-02-16T19:49:20.974804:Starting permutation 374
170216-19:49:21,496 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 375
170216-19:49:21,498 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 376
170216-19:49:21,498 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 377
170216-19:49:21,499 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 378
170216-19:49:21,500 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 379
170216-19:49:21,500 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 380
170216-19:49:21,501 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 381
170216-19:49:21,501 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 382
170216-19:49:21,502 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 383
170216-19:49:21,502 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 384
170216-19:49:21,503 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 385
170216-19:49:21,503 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 386
170216-19:49:21,504 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 387
170216-19:49:21,504 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 388
170216-19:49:21,505 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 389
170216-19:49:21,510 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 390
170216-19:49:21,511 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 391
170216-19:49:21,511 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 392
170216-19:49:21,512 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 393
170216-19:49:21,512 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 394
170216-19:49:21,513 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 395
170216-19:49:21,513 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 396
170216-19:49:21,514 interface INFO:
stdout 2017-02-16T19:49:21.496774:Starting permutation 397
170216-19:49:22,14 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 398
170216-19:49:22,15 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 399
170216-19:49:22,16 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 400
170216-19:49:22,17 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 401
170216-19:49:22,19 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 402
170216-19:49:22,20 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 403
170216-19:49:22,21 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 404
170216-19:49:22,22 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 405
170216-19:49:22,23 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 406
170216-19:49:22,29 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 407
170216-19:49:22,30 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 408
170216-19:49:22,31 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 409
170216-19:49:22,32 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 410
170216-19:49:22,33 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 411
170216-19:49:22,34 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 412
170216-19:49:22,35 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 413
170216-19:49:22,46 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 414
170216-19:49:22,47 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 415
170216-19:49:22,48 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 416
170216-19:49:22,49 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 417
170216-19:49:22,50 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 418
170216-19:49:22,51 interface INFO:
stdout 2017-02-16T19:49:22.014804:Starting permutation 419
170216-19:49:22,552 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 420
170216-19:49:22,553 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 421
170216-19:49:22,554 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 422
170216-19:49:22,554 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 423
170216-19:49:22,555 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 424
170216-19:49:22,556 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 425
170216-19:49:22,556 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 426
170216-19:49:22,557 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 427
170216-19:49:22,558 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 428
170216-19:49:22,558 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 429
170216-19:49:22,559 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 430
170216-19:49:22,559 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 431
170216-19:49:22,560 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 432
170216-19:49:22,570 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 433
170216-19:49:22,570 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 434
170216-19:49:22,571 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 435
170216-19:49:22,571 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 436
170216-19:49:22,572 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 437
170216-19:49:22,573 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 438
170216-19:49:22,574 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 439
170216-19:49:22,574 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 440
170216-19:49:22,575 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 441
170216-19:49:22,575 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 442
170216-19:49:22,576 interface INFO:
stdout 2017-02-16T19:49:22.552603:Starting permutation 443
170216-19:49:23,78 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 444
170216-19:49:23,79 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 445
170216-19:49:23,80 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 446
170216-19:49:23,81 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 447
170216-19:49:23,83 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 448
170216-19:49:23,84 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 449
170216-19:49:23,85 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 450
170216-19:49:23,86 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 451
170216-19:49:23,91 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 452
170216-19:49:23,93 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 453
170216-19:49:23,94 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 454
170216-19:49:23,95 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 455
170216-19:49:23,96 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 456
170216-19:49:23,106 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 457
170216-19:49:23,107 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 458
170216-19:49:23,108 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 459
170216-19:49:23,109 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 460
170216-19:49:23,110 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 461
170216-19:49:23,111 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 462
170216-19:49:23,113 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 463
170216-19:49:23,113 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 464
170216-19:49:23,114 interface INFO:
stdout 2017-02-16T19:49:23.078101:Starting permutation 465
170216-19:49:23,616 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 466
170216-19:49:23,617 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 467
170216-19:49:23,618 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 468
170216-19:49:23,618 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 469
170216-19:49:23,619 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 470
170216-19:49:23,620 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 471
170216-19:49:23,621 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 472
170216-19:49:23,622 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 473
170216-19:49:23,622 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 474
170216-19:49:23,623 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 475
170216-19:49:23,623 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 476
170216-19:49:23,624 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 477
170216-19:49:23,630 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 478
170216-19:49:23,631 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 479
170216-19:49:23,632 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 480
170216-19:49:23,632 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 481
170216-19:49:23,633 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 482
170216-19:49:23,633 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 483
170216-19:49:23,634 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 484
170216-19:49:23,634 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 485
170216-19:49:23,635 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 486
170216-19:49:23,635 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 487
170216-19:49:23,636 interface INFO:
stdout 2017-02-16T19:49:23.616195:Starting permutation 488
170216-19:49:24,138 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 489
170216-19:49:24,139 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 490
170216-19:49:24,139 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 491
170216-19:49:24,140 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 492
170216-19:49:24,140 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 493
170216-19:49:24,141 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 494
170216-19:49:24,141 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 495
170216-19:49:24,142 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 496
170216-19:49:24,142 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 497
170216-19:49:24,143 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 498
170216-19:49:24,144 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 499
170216-19:49:24,145 interface INFO:
stdout 2017-02-16T19:49:24.138095:Starting permutation 500
170216-19:49:24,146 interface INFO:
stdout 2017-02-16T19:49:24.138095:Critical Value for: tbss__vox_corrp_tstat1 is: 9.29613
170216-19:49:24,147 interface INFO:
stdout 2017-02-16T19:49:24.138095:Critical Value for: tbss__tfce_corrp_tstat1 is: 5572.7
170216-19:49:24,147 interface INFO:
stdout 2017-02-16T19:49:24.138095:Finished, exiting.
Out[115]:
f_corrected_p_files = []
f_p_files = []
fstat_files = []
t_corrected_p_files = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Randomise/393fecf255fa7f15245cd7fa32e0d3c0/tbss__tfce_corrp_tstat1.nii.gz']
t_p_files = []
tstat_files = ['/home/vagrant/fmri-analysis-vm/analysis/firstlevel/nipype_mem/nipype-interfaces-fsl-model-Randomise/393fecf255fa7f15245cd7fa32e0d3c0/tbss__tstat1.nii.gz']
In [116]:
nilearn.plotting.plot_stat_map(randomise_results.outputs.t_corrected_p_files[0], threshold=0.95)
Out[116]:
<nilearn.plotting.displays.OrthoSlicer at 0x7f2dae9958d0>
In [117]:
fig = nilearn.plotting.plot_stat_map(randomise_results.outputs.tstat_files[0], alpha=0.5, cut_coords=(-21, 0, 18))
fig.add_contours(randomise_results.outputs.t_corrected_p_files[0], levels=[0.95], colors='w')
In [84]:
nilearn.plotting.plot_stat_map?
In [ ]:
Content source: poldrack/fmri-analysis-vm
Similar notebooks: