In [35]:

    

import matplotlib
import numpy as np
import matplotlib.pyplot as plt
from scipy import stats
from scipy import io
import scipy.io as sio
%matplotlib inline 
import pylab
import csv
from Tkinter import Tk
from tkFileDialog import askopenfilename
from tkFileDialog import askdirectory
import nibabel as nb
from scipy.interpolate import interp1d
from scipy import ndimage


    

In [36]:

    

filenameM='/home/sophie/RegionList'
with open(filenameM) as f:
    content = f.readlines()
Names=[Line.split('\t') for Line in content]
RegionName=[Names[i][0] for i in range(75)]
Num=[int(Names[i][2]) for i in range(75)]


    

In [26]:

    

# from http://stackoverflow.com/questions/3579568/choosing-a-file-in-python-with-simple-dialog
from Tkinter import Tk
from tkFileDialog import askopenfilename

Tk().withdraw() # we don't want a full GUI, so keep the root window from appearing
filenameM = askopenfilename() # show an "Open" dialog box and return the path to the selected file
print(filenameM)


    

    




/media/sophie/470fddca-e336-42c7-9d91-b91361d994ea/100697seriesGood/100697series/100697Registration/JFRCTemplate03_2018.nii

In [27]:

    

img1 = nb.load(filenameM)
Masks = img1.get_data()
Sm=Masks.shape
Masks=np.array(Masks)


    

In [37]:

    

LargerRegionDic={'':'','AME_R':'OL','LO_R':'OL','NO':'CX','BU_R':'CX','PB':'CX','LH_R':'LH','LAL_R':'LX','SAD':'PENP'
               ,'CAN_R':'PENP','AMMC_R':'PENP','ICL_R':'INP','VES_R':'VMNP','IB_R':'INP','ATL_R':'INP','CRE_R':'INP'
               ,'MB_PED_R':'MB','MB_VL_R':'MB','MB_ML_R':'MB','FLA_R':'PENP','LOP_R':'OL','EB':'CX','AL_R':'AL',
                'ME_R':'OL','FB':'CX','SLP_R':'SNP','SIP_R':'SNP','SMP_R':'SNP','AVLP_R':'VLNP','PVLP_R':'VLNP',
                'IVLP_R':'VLNP','PLP_R':'VLNP','AOTU_R':'VLNP','GOR_R':'VMNP','MB_CA_R':'MB','SPS_R':'VMNP',
                'IPS_R':'VMNP','SCL_R':'INP','EPA_R':'VMNP','GNG':'GNG','PRW':'PENP','GA_R':'LX','AME_L':'OL'
                ,'LO_L':'OL','BU_L':'CX','LH_L':'LH','LAL_L':'LX','CAN_L':'PENP','AMMC_L':'PENP','ICL_L':'INP',
                'VES_L':'VMNP','IB_L':'INP','ATL_L':'INP','CRE_L':'INP','MB_PED_L':'MB','MB_VL_L':'MB',
                'MB_ML_L':'MB','FLA_L':'PENP','LOP_L':'OL','AL_L':'AL','ME_L':'OL','SLP_L':'SNP','SIP_L':'SNP',
                'SMP_L':'SNP','AVLP_L':'VLNP','PVLP_L':'VLNP','IVLP_L':'VLNP','PLP_L':'VLNP','AOTU_L':'VLNP',
                'GOR_L':'VMNP','MB_CA_L':'MB','SPS_L':'VMNP','IPS_L':'VMNP','SCL_L':'INP','EPA_L':'VMNP','GA_L':'LX'}


    

In [38]:

    

LargerRegionInd={ 'OL':1,'VLNP':2,'VMNP':3,'AL':4,'MB':5,'LH':6,'SNP':7,'CX':8,'LX':9,'INP':10,'PENP':11,'GNG':12,'':13}


    

In [39]:

    

SmallRegionLargeId={k: LargerRegionInd[v] for (k,v) in LargerRegionDic.items()}


    

In [40]:

    

SmallRegionLargeId['AL_L']


    

    
Out[40]:





4

In [33]:

    

Sm


    

    
Out[33]:





(1024, 512, 44, 1)

In [42]:

    

MaskLargeReg=np.zeros([Sm[0],Sm[1],Sm[2],12])
for k in range(13):
    for j in range(74):
        if SmallRegionLargeId[RegionName[j+1]]==k:
            #MaskLargeReg[:,:,:,k-1]=MaskLargeReg[:,:,:,k-1]+Masks[:,:,:,Num[j+1]-1]
            print(Num[j+1])
            #print(RegionName[j+1])
            print(k)


    

    




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In [21]:

    

NewName='/'.join(filenameM.split('/')[:-1])+'/JFRCTransformedLarge.nii'


    

In [22]:

    

NewName


    

    
Out[22]:





'/media/sophie/db554c18-e3eb-41e2-afad-7de1c92bf4a5/ArclightCombo/100051/JFRCTransformedLarge.nii'

In [23]:

    

nim=nb.Nifti1Image(MaskLargeReg,np.eye(4))
nb.save(nim,NewName)