roi | Python Fiddle

"""
Created on Thu Mar 24 16:06:08 2016
Generate ROIs
@author: Jonika
"""
import os
import subprocess

os.chdir("/home/Jonika/Documents/NKI/Data")
mypath=os.getcwd() #saves directory
subjects= os.listdir(mypath)
for subject in subjects:
    mri="/home/Jonika/Documents/network_folder/NKI/Data/"+subject+"/mri"
    bedpost="/home/Jonika/Documents/network_folder/NKI/Data/1013090/DTI.bedpostX"
    xfms="/home/Jonika/Documents/network_folder/NKI/Data/1013090/DTI.bedpostX/xfms"
    os.chdir(mri)
    subprocess.call(["mri_convert", "brain.mgz", "brain.nii" ])
    subprocess.call(["mri_convert", "aparc.a2009s+aseg.mgz", "aparc.a2009s+aseg.nii" ])
    os.chdir(xfms)
    subprocess.call(["flirt", "-in", "/home/Jonika/Documents/NKI/Data/"+subject+"/DTI/nodif_brain.nii.gz", "-ref", "/home/Jonika/Documents/NKI/Data/"+subject+"/mri/brain.nii", "-omat", "diff2str.mat", "-dof", "12"])
    subprocess.call(["convert_xfm", "-omat", "str2diff.mat", "-inverse", "diff2str.mat"])
    subprocess.call(["flirt", "-in", "brain.nii", "-ref", "/home/Jonika/Documents/NKI/Data/"+subject+"/DTI/nodif_brain.nii.gz", "-applyxfm", "-init", "str2diff.mat", "-out", "str2brain"])
    rois={"left_amydgala": "18", "right_amygdala":"54","left_superior_frontal_gyrus":"11116", "right_superior_frontal_gyrus":"12116","left_front_inf_opercular": "11112","left_front_inf_orbital": "11113", "left_front_inf_triangul":"11114", "right_front_inf_opercular": "12112", "right_front_inf_orbital": "12113", "right_front_inf_triangul": "12114","left_medial_orbitofrontal":" ", "right_medial_orbitofrontal": " ", "left_insula": " ", "right_insula":" ", "left_rostral_anterior_cingulate": " ", "right_rostral_anterior_cingulate": " ", "left_caudal_anterior_cingulate": " ", "right_caudal_anterior_cingulate": " ", "left_accumbens": "26", "right_accumbens": "58", "left_ventral_dc": "28", "right_ventral_dc": "60"}    
    for roi in rois:
    	subprocess.call(["fslmaths", "-dt", "int", "/home/Jonika/Documents/NKI/Data/"+subject+"/mri/aparc.a2009s+aseg.mgz", "-thr", rois[roi], "-uthr", rois[roi], roi+"_mask", "-odt", "int"])
        subprocess.call(["flirt", "-in", roi+"_mask", "ref", "/home/Jonika/Documents/NKI/Data/"+subject+"/DTI/nodif_brain.nii.gz", "-applyxfm", "-init", "str2diff.mat", "-out", roi+"_registered"])

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