I have run the scores pipeline on guilimin (some of the subjects have failed) and now I want to cluster them by their stability maps, seed maps and other available metrics.
Some of the functions I will be using here are part of a little package I have started to wrap things together that I am reusing constantly. This makes it less straight forward to run this notebook on a different machine but makes the whole thing faster and cleaner for me. The package is located here.
In [15]:
import os
import sys
import nibabel as nib
import brainbox as bb
In [16]:
in_path = '/data1/abide/Out/Remote/some_failed/out'
out_path = '/data1/abide/Analysis/Remote/some_missing'
In [17]:
# Network to investigate - in the case of multi-network files
network = 0
# Metric to load
metric = 'dual_regression'
# Scale to investigate - chooses the hierarchical cutoff
scale = 0
In [18]:
file_dict = bb.fileOps.grab_files(in_path, '.nii.gz')
In [19]:
file_dict
Out[19]:
{'dir': ['dual_regression',
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'UCLA_1_0051279_session_1_run1_stability_inter',
'Olin_0050120_session_1_run1_stability_inter',
'UCLA_1_0051223_session_1_run1_stability_inter',
'NYU_0050984_session_1_run1_stability_inter',
'NYU_0051067_session_1_run1_stability_inter',
'KKI_0050797_session_1_run1_stability_inter',
'NYU_0051012_session_1_run1_stability_inter',
'USM_0050500_session_1_run1_stability_inter',
'KKI_0050772_session_1_run1_stability_inter',
'KKI_0050824_session_1_run1_stability_inter',
'Pitt_0050027_session_1_run1_stability_inter',
'Trinity_0050240_session_1_run1_stability_inter',
'OHSU_0050169_session_1_run3_stability_inter',
'UCLA_2_0051306_session_1_run1_stability_inter',
'NYU_0051071_session_1_run1_stability_inter',
'NYU_0051085_session_1_run1_stability_inter',
'USM_0050437_session_1_run1_stability_inter',
'OHSU_0050146_session_1_run2_stability_inter',
'Leuven_2_0050739_session_1_run1_stability_inter',
'NYU_0051036_session_1_run1_stability_inter',
'Caltech_0051467_session_1_run1_stability_inter',
'UCLA_1_0051211_session_1_run1_stability_inter',
'SDSU_0050186_session_1_run1_stability_inter',
'Olin_0050117_session_1_run1_stability_inter',
'Pitt_0050045_session_1_run1_stability_inter',
'NYU_0051086_session_1_run1_stability_inter',
'OHSU_0050142_session_1_run3_stability_inter',
'UCLA_1_0051252_session_1_run1_stability_inter',
'NYU_0051149_session_1_run1_stability_inter',
'Stanford_0051161_session_1_run1_stability_inter',
'NYU_0051058_session_1_run1_stability_inter',
'SDSU_0050203_session_1_run1_stability_inter',
'USM_0050489_session_1_run1_stability_inter',
'NYU_0051147_session_1_run1_stability_inter',
'Leuven_2_0050726_session_1_run1_stability_inter',
'UCLA_2_0051292_session_1_run1_stability_inter',
'NYU_0050990_session_1_run1_stability_inter',
'SDSU_0050185_session_1_run1_stability_inter',
'MaxMun_c_0051344_session_1_run1_stability_inter',
'Stanford_0051182_session_1_run1_stability_inter',
'NYU_0051000_session_1_run1_stability_inter',
'USM_0050455_session_1_run1_stability_inter',
'UCLA_1_0051280_session_1_run1_stability_inter',
'Pitt_0050052_session_1_run1_stability_inter',
'NYU_0051048_session_1_run1_stability_inter',
'NYU_0051047_session_1_run1_stability_inter',
'NYU_0051045_session_1_run1_stability_inter',
'Pitt_0050053_session_1_run1_stability_inter',
'Olin_0050116_session_1_run1_stability_inter',
'Trinity_0050243_session_1_run1_stability_inter',
'OHSU_0050142_session_1_run1_stability_inter',
'USM_0050492_session_1_run1_stability_inter',
'SDSU_0050204_session_1_run1_stability_inter',
'USM_0050451_session_1_run1_stability_inter',
'KKI_0050823_session_1_run1_stability_inter',
'USM_0050433_session_1_run1_stability_inter',
'Caltech_0051489_session_1_run1_stability_inter',
'UCLA_1_0051263_session_1_run1_stability_inter',
'NYU_0051117_session_1_run1_stability_inter',
'MaxMun_d_0051357_session_1_run1_stability_inter',
'OHSU_0050161_session_1_run2_stability_inter',
'SDSU_0050187_session_1_run1_stability_inter',
'OHSU_0050143_session_1_run1_stability_inter',
'SDSU_0050189_session_1_run1_stability_inter',
'OHSU_0050159_session_1_run3_stability_inter',
'Caltech_0051460_session_1_run1_stability_inter',
'SBL_0051573_session_1_run1_stability_inter',
'Stanford_0051176_session_1_run1_stability_inter',
'USM_0050514_session_1_run1_stability_inter',
'USM_0050510_session_1_run1_stability_inter',
'Stanford_0051180_session_1_run1_stability_inter',
'OHSU_0050168_session_1_run2_stability_inter',
'USM_0050501_session_1_run1_stability_inter',
'MaxMun_a_0051366_session_1_run1_stability_inter',
'Olin_0050105_session_1_run1_stability_inter',
'MaxMun_a_0051365_session_1_run1_stability_inter',
'Leuven_2_0050752_session_1_run1_stability_inter',
'Olin_0050132_session_1_run1_stability_inter',
'Leuven_2_0050733_session_1_run1_stability_inter',
'SBL_0051562_session_1_run1_stability_inter',
'Leuven_1_0050698_session_1_run1_stability_inter',
'NYU_0051003_session_1_run1_stability_inter',
'SDSU_0050190_session_1_run1_stability_inter',
'Stanford_0051189_session_1_run1_stability_inter',
'UCLA_1_0051266_session_1_run1_stability_inter',
'NYU_0051112_session_1_run1_stability_inter',
'KKI_0050804_session_1_run1_stability_inter',
'KKI_0050777_session_1_run1_stability_inter',
'USM_0050491_session_1_run1_stability_inter',
'KKI_0050807_session_1_run1_stability_inter',
'MaxMun_d_0051356_session_1_run1_stability_inter',
'NYU_0050986_session_1_run1_stability_inter',
'Trinity_0050267_session_1_run1_stability_inter',
'OHSU_0050168_session_1_run3_stability_inter',
'Leuven_2_0050742_session_1_run1_stability_inter',
'KKI_0050774_session_1_run1_stability_inter',
'CMU_a_0050653_session_1_run1_stability_inter',
'USM_0050499_session_1_run1_stability_inter',
'SDSU_0050196_session_1_run1_stability_inter',
'OHSU_0050142_session_1_run2_stability_inter',
'KKI_0050781_session_1_run1_stability_inter',
'Stanford_0051187_session_1_run1_stability_inter',
'SBL_0051584_session_1_run1_stability_inter',
'Trinity_0050248_session_1_run1_stability_inter',
'KKI_0050821_session_1_run1_stability_inter',
'NYU_0051061_session_1_run1_stability_inter',
'OHSU_0050146_session_1_run3_stability_inter',
'NYU_0051039_session_1_run1_stability_inter',
'NYU_0051156_session_1_run1_stability_inter',
'UCLA_2_0051300_session_1_run1_stability_inter',
'Stanford_0051194_session_1_run1_stability_inter',
'SDSU_0050205_session_1_run1_stability_inter',
'USM_0050490_session_1_run1_stability_inter',
'Olin_0050133_session_1_run1_stability_inter',
'Caltech_0051479_session_1_run1_stability_inter',
'NYU_0050982_session_1_run1_stability_inter',
'USM_0050504_session_1_run1_stability_inter',
'MaxMun_a_0051371_session_1_run1_stability_inter',
'Caltech_0051472_session_1_run1_stability_inter',
'UCLA_1_0051255_session_1_run1_stability_inter',
'KKI_0050794_session_1_run1_stability_inter',
'Stanford_0051167_session_1_run1_stability_inter',
'Leuven_2_0050757_session_1_run1_stability_inter',
'CMU_b_0050648_session_1_run1_stability_inter',
'NYU_0050980_session_1_run1_stability_inter',
'USM_0050453_session_1_run1_stability_inter',
'NYU_0051060_session_1_run1_stability_inter',
'SDSU_0050184_session_1_run1_stability_inter',
'NYU_0050978_session_1_run1_stability_inter',
'USM_0050457_session_1_run1_stability_inter',
'UCLA_2_0051313_session_1_run1_stability_inter',
'MaxMun_d_0051331_session_1_run1_stability_inter',
'OHSU_0050150_session_1_run2_stability_inter',
'Trinity_0050246_session_1_run1_stability_inter',
'UCLA_1_0051215_session_1_run1_stability_inter',
'Pitt_0050034_session_1_run1_stability_inter',
'MaxMun_d_0051354_session_1_run1_stability_inter',
'MaxMun_a_0051318_session_1_run1_stability_inter',
'Trinity_0050249_session_1_run1_stability_inter',
'UCLA_2_0051301_session_1_run1_stability_inter',
'UCLA_2_0051293_session_1_run1_stability_inter',
'Olin_0050119_session_1_run1_stability_inter',
'Leuven_1_0050685_session_1_run1_stability_inter',
'Stanford_0051169_session_1_run1_stability_inter',
'OHSU_0050168_session_1_run1_stability_inter',
'NYU_0050998_session_1_run1_stability_inter',
'NYU_0050997_session_1_run1_stability_inter',
'Leuven_1_0050702_session_1_run1_stability_inter',
'CMU_a_0050656_session_1_run1_stability_inter',
'Leuven_1_0050682_session_1_run1_stability_inter',
'NYU_0050953_session_1_run1_stability_inter',
'SDSU_0050182_session_1_run1_stability_inter',
'MaxMun_d_0051361_session_1_run1_stability_inter',
'KKI_0050808_session_1_run1_stability_inter',
'USM_0050436_session_1_run1_stability_inter',
'USM_0050481_session_1_run1_stability_inter',
'NYU_0050954_session_1_run1_stability_inter',
'Stanford_0051183_session_1_run1_stability_inter',
'NYU_0050975_session_1_run1_stability_inter',
'Trinity_0050250_session_1_run1_stability_inter',
'MaxMun_c_0051346_session_1_run1_stability_inter',
'SDSU_0050197_session_1_run1_stability_inter',
'MaxMun_d_0051351_session_1_run1_stability_inter',
'SDSU_0050191_session_1_run1_stability_inter',
'USM_0050462_session_1_run1_stability_inter',
'NYU_0051093_session_1_run1_stability_inter',
'MaxMun_c_0051334_session_1_run1_stability_inter',
'Olin_0050115_session_1_run1_stability_inter',
'Stanford_0051170_session_1_run1_stability_inter',
'KKI_0050805_session_1_run1_stability_inter',
'Stanford_0051198_session_1_run1_stability_inter',
'Stanford_0051165_session_1_run1_stability_inter',
'MaxMun_c_0051340_session_1_run1_stability_inter',
'MaxMun_d_0051360_session_1_run1_stability_inter',
'OHSU_0050161_session_1_run3_stability_inter',
'Pitt_0050039_session_1_run1_stability_inter',
'MaxMun_d_0051353_session_1_run1_stability_inter',
'Pitt_0050054_session_1_run1_stability_inter',
'CMU_b_0050643_session_1_run1_stability_inter',
'MaxMun_a_0051369_session_1_run1_stability_inter',
'Leuven_2_0050722_session_1_run1_stability_inter',
'NYU_0051095_session_1_run1_stability_inter',
'Leuven_1_0050709_session_1_run1_stability_inter',
'USM_0050484_session_1_run1_stability_inter',
'KKI_0050803_session_1_run1_stability_inter',
'UCLA_2_0051312_session_1_run1_stability_inter',
'USM_0050444_session_1_run1_stability_inter',
'Caltech_0051474_session_1_run1_stability_inter',
'USM_0050432_session_1_run1_stability_inter',
'UCLA_1_0051267_session_1_run1_stability_inter',
'Caltech_0051465_session_1_run1_stability_inter',
'UCLA_1_0051253_session_1_run1_stability_inter',
'KKI_0050800_session_1_run1_stability_inter',
'UCLA_1_0051254_session_1_run1_stability_inter',
'MaxMun_c_0051343_session_1_run1_stability_inter',
'Pitt_0050051_session_1_run1_stability_inter',
'SDSU_0050183_session_1_run1_stability_inter',
'Pitt_0050004_session_1_run1_stability_inter',
'Olin_0050112_session_1_run1_stability_inter',
'Caltech_0051466_session_1_run1_stability_inter',
'UCLA_1_0051275_session_1_run1_stability_inter',
'Pitt_0050050_session_1_run1_stability_inter',
'Trinity_0050270_session_1_run1_stability_inter',
'OHSU_0050169_session_1_run1_stability_inter',
'OHSU_0050147_session_1_run1_stability_inter',
'OHSU_0050160_session_1_run1_stability_inter',
'SDSU_0050212_session_1_run1_stability_inter',
'USM_0050526_session_1_run1_stability_inter',
'USM_0050448_session_1_run1_stability_inter',
'UCLA_1_0051258_session_1_run1_stability_inter',
'UCLA_2_0051308_session_1_run1_stability_inter',
'Stanford_0051184_session_1_run1_stability_inter',
'KKI_0050798_session_1_run1_stability_inter',
'KKI_0050820_session_1_run1_stability_inter',
'Caltech_0051456_session_1_run1_stability_inter',
'NYU_0050961_session_1_run1_stability_inter',
'Stanford_0051164_session_1_run1_stability_inter',
'UCLA_1_0051217_session_1_run1_stability_inter',
'NYU_0051044_session_1_run1_stability_inter',
'OHSU_0050171_session_1_run2_stability_inter',
'Trinity_0051138_session_1_run1_stability_inter',
'Leuven_2_0050751_session_1_run1_stability_inter',
'NYU_0050979_session_1_run1_stability_inter',
'Stanford_0051186_session_1_run1_stability_inter',
'Trinity_0050252_session_1_run1_stability_inter',
'UCLA_1_0051261_session_1_run1_stability_inter',
'Pitt_0050037_session_1_run1_stability_inter',
'NYU_0051080_session_1_run1_stability_inter',
'NYU_0051028_session_1_run1_stability_inter',
'MaxMun_b_0051326_session_1_run1_stability_inter',
'Trinity_0050269_session_1_run1_stability_inter',
'Leuven_2_0050749_session_1_run1_stability_inter',
'Leuven_2_0050731_session_1_run1_stability_inter',
'Trinity_0050245_session_1_run1_stability_inter',
'Stanford_0051196_session_1_run1_stability_inter',
'USM_0050472_session_1_run1_stability_inter',
'Leuven_2_0050730_session_1_run1_stability_inter',
'UCLA_1_0051234_session_1_run1_stability_inter',
'Caltech_0051470_session_1_run1_stability_inter',
'NYU_0051014_session_1_run1_stability_inter',
'KKI_0050796_session_1_run1_stability_inter',
'Caltech_0051468_session_1_run1_stability_inter',
'Trinity_0050268_session_1_run1_stability_inter',
'MaxMun_d_0051352_session_1_run1_stability_inter',
'USM_0050502_session_1_run1_stability_inter',
'Trinity_0050253_session_1_run1_stability_inter',
'USM_0050479_session_1_run1_stability_inter',
'CMU_b_0050667_session_1_run1_stability_inter',
'USM_0050494_session_1_run1_stability_inter',
'Olin_0050121_session_1_run1_stability_inter',
'KKI_0050782_session_1_run1_stability_inter',
'USM_0050456_session_1_run1_stability_inter',
'KKI_0050810_session_1_run1_stability_inter',
'Pitt_0050007_session_1_run1_stability_inter',
'Pitt_0050019_session_1_run1_stability_inter',
'CMU_a_0050642_session_1_run1_stability_inter',
'SBL_0051559_session_1_run1_stability_inter',
'OHSU_0050152_session_1_run1_stability_inter',
'Stanford_0051168_session_1_run1_stability_inter',
'Leuven_2_0050725_session_1_run1_stability_inter',
'Caltech_0051482_session_1_run1_stability_inter',
'UCLA_2_0051309_session_1_run1_stability_inter',
'NYU_0051002_session_1_run1_stability_inter',
'UCLA_1_0051205_session_1_run1_stability_inter',
'UCLA_1_0051281_session_1_run1_stability_inter',
'OHSU_0050163_session_1_run1_stability_inter',
'Pitt_0050038_session_1_run1_stability_inter',
'USM_0050440_session_1_run1_stability_inter',
'CMU_b_0050652_session_1_run1_stability_inter',
'UCLA_1_0051264_session_1_run1_stability_inter',
'NYU_0051027_session_1_run1_stability_inter',
'OHSU_0050146_session_1_run1_stability_inter',
'Stanford_0051191_session_1_run1_stability_inter',
'USM_0050512_session_1_run1_stability_inter',
'Trinity_0050232_session_1_run1_stability_inter',
'Caltech_0051481_session_1_run1_stability_inter',
'Stanford_0051193_session_1_run1_stability_inter',
'NYU_0050995_session_1_run1_stability_inter',
'NYU_0051096_session_1_run1_stability_inter',
'Leuven_2_0050723_session_1_run1_stability_inter',
...]}
In [22]:
array_dict = {}
drops = []
for idx, sub in enumerate(file_dict['sub_name']):
sub_dir = file_dict['dir'][idx]
sub_path = file_dict['path'][idx]
try:
tmp_data = nib.load(sub_path).get_data()
except:
if not sub_dir in drops:
drops.append(sub_dir)
continue
if len(shape(tmp_data)) > 3:
tmp_net = tmp_data[...,network]
else:
tmp_net = tmp_data
tmp_flat = np.ndarray.flatten(tmp_net)
# See if the metric has been stored yet
if not sub_dir in array_dict.keys():
array_dict[sub_dir] = tmp_flat[:, None]
else:
array_dict[sub_dir] = np.concatenate((array_dict[sub_dir], tmp_flat[:, None]), axis=1)
print('These things were unavailable:\n')
print(drops)
In [23]:
Out[23]:
{'dual_regression': array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
...,
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.]]),
'rmap_cores': array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
...,
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.]]),
'rmap_part': array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
...,
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.]]),
'stability_maps': array([[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
...,
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.],
[ 0., 0., 0., ..., 0., 0., 0.]])}
In [ ]:
Content source: surchs/Logbooks
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