def get_subcort(subj):
bash_scripts_dir = '/crtx1/zgreenberg/scripts/bash'
python_scripts_dir = '/crtx1/zgreenberg/scripts/python'
subjAscii_dir = ('/crtx1/zgreenberg/subjects/%s/ascii/' % (subj))
# nav to scripts dir to call aseg2srf
os.chdir(bash_scripts_dir)
# tessellate all subjects freesurfer subcortical segmentations
os.system(
'./aseg2srf.sh -s "%s" -l "4 5 10 11 12 13 17 18 26 28 43 44 49 50 51 52 53 54 58 60 14 15 16"'
% (subj))
# nav to dir with ascii outputs for each subcortical segmented surface
os.chdir(subjAscii_dir)
# get list of all .srf files and change fname to .asc
srf_list = [fname for fname in os.listdir(os.getcwd())]
asc_list = [fname.replace('.srf', '.asc') for fname in srf_list]
asc_list.sort()
for fname in srf_list:
new_fname = fname.replace('.srf', '.asc')
os.system("mv %s %s" % (fname, new_fname))
# convert all ascii subcortical meshes to matlab vert, tri coords
print "::: Converting all ascii segmentations to matlab tri-vert :::"
subcort = 'aseg_058.asc'
nuc = 'rAcumb'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_054.asc'
nuc = 'rAmgd'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_050.asc'
nuc = 'rCaud'
subcortFs2mlab(subcort, nuc)
nuc = 'rGP'
subcort = 'aseg_052.asc'
subcortFs2mlab(subcort, nuc)
nuc = 'rHipp'
subcort = 'aseg_053.asc'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_051.asc'
nuc = 'rPut'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_049.asc'
nuc = 'rThal'
subcortFs2mlab(subcort, nuc)
nuc = 'rLatVent'
subcort = 'aseg_043.asc'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_044.asc'
nuc = 'rInfLatVent'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_060.asc'
nuc = 'rVentDienceph'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_004.asc'
nuc = 'lLatVent'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_005.asc'
nuc = 'lInfLatVent'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_010.asc'
nuc = 'lThal'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_011.asc'
nuc = 'lCaud'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_012.asc'
nuc = 'lPut'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_013.asc'
nuc = 'lGP'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_017.asc'
nuc = 'lHipp'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_018.asc'
nuc = 'lAmgd'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_026.asc'
nuc = 'lAcumb'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_028.asc'
nuc = 'lVentDienceph'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_014.asc'
nuc = 'lThirdVent'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_015.asc'
nuc = 'lFourthVent'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_016.asc'
nuc = 'lBrainStem'
subcortFs2mlab(subcort, nuc)
def get_trivert(subj):
subjects_dir = '/crtx1/zgreenberg/subjects'
os.system('cd %s/%s/ascii/' % (subjects_dir, subj))
# convert all ascii subcortical meshes to matlab vert, tri coords
subcort = 'aseg_rAcumb.asc'
nuc = 'rAcumb'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_rAmgd.asc'
nuc = 'rAmgd'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_rCaud.asc'
nuc = 'rCaud'
subcortFs2mlab(subcort, nuc)
nuc = 'rGP'
subcort = 'aseg_rGP.asc'
subcortFs2mlab(subcort, nuc)
nuc = 'rHipp'
subcort = 'aseg_rHipp.asc'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_rPut.asc'
subcort = 'aseg_rPut.asc'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_rThal.asc'
nuc = 'rThal'
subcortFs2mlab(subcort, nuc)
nuc = 'rLatVent'
subcort = 'aseg_rLatVent.asc'
subcortFs2mlab(subcort, nuc)
subcort = 'aseg_rInfLatVent.asc'
nuc = 'rInfLatVent'
subcortFs2mlab(subcort, nuc)
def get_subcort(subj):
bash_scripts_dir = '/crtx1/zgreenberg/scripts/bash';
python_scripts_dir = '/crtx1/zgreenberg/scripts/python';
subjAscii_dir = ('/crtx1/zgreenberg/subjects/%s/ascii/' %(subj));
# nav to scripts dir to call aseg2srf
os.chdir(bash_scripts_dir);
# tessellate all subjects freesurfer subcortical segmentations
os.system('./aseg2srf.sh -s "%s" -l "4 5 10 11 12 13 17 18 26 28 43 44 49 50 51 52 53 54 58 60 14 15 16"' %(subj));
# nav to dir with ascii outputs for each subcortical segmented surface
os.chdir(subjAscii_dir);
# get list of all .srf files and change fname to .asc
srf_list = [fname for fname in os.listdir(os.getcwd())];
asc_list = [fname.replace('.srf', '.asc') for fname in srf_list];
asc_list.sort();
for fname in srf_list:
new_fname = fname.replace('.srf', '.asc');
os.system("mv %s %s" %(fname, new_fname));
# convert all ascii subcortical meshes to matlab vert, tri coords
print "::: Converting all ascii segmentations to matlab tri-vert :::";
subcort = 'aseg_058.asc';
nuc = 'rAcumb';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_054.asc';
nuc = 'rAmgd';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_050.asc';
nuc = 'rCaud';
subcortFs2mlab(subcort,nuc);
nuc = 'rGP';
subcort = 'aseg_052.asc';
subcortFs2mlab(subcort,nuc);
nuc = 'rHipp';
subcort = 'aseg_053.asc';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_051.asc';
nuc = 'rPut';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_049.asc';
nuc = 'rThal';
subcortFs2mlab(subcort,nuc);
nuc = 'rLatVent';
subcort = 'aseg_043.asc';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_044.asc';
nuc = 'rInfLatVent';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_060.asc';
nuc = 'rVentDienceph';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_004.asc';
nuc = 'lLatVent';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_005.asc';
nuc = 'lInfLatVent';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_010.asc';
nuc = 'lThal';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_011.asc';
nuc = 'lCaud';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_012.asc';
nuc = 'lPut';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_013.asc';
nuc = 'lGP';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_017.asc';
nuc = 'lHipp';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_018.asc';
nuc = 'lAmgd';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_026.asc';
nuc = 'lAcumb';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_028.asc';
nuc = 'lVentDienceph';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_014.asc';
nuc = 'lThirdVent';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_015.asc';
nuc = 'lFourthVent';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_016.asc';
nuc = 'lBrainStem';
subcortFs2mlab(subcort,nuc);
def get_trivert(subj):
subjects_dir = '/crtx1/zgreenberg/subjects';
os.system('cd %s/%s/ascii/' %(subjects_dir, subj));
# convert all ascii subcortical meshes to matlab vert, tri coords
subcort = 'aseg_rAcumb.asc';
nuc = 'rAcumb';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_rAmgd.asc';
nuc = 'rAmgd';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_rCaud.asc';
nuc = 'rCaud';
subcortFs2mlab(subcort,nuc);
nuc = 'rGP';
subcort = 'aseg_rGP.asc';
subcortFs2mlab(subcort,nuc);
nuc = 'rHipp';
subcort = 'aseg_rHipp.asc';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_rPut.asc';
subcort = 'aseg_rPut.asc';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_rThal.asc';
nuc = 'rThal';
subcortFs2mlab(subcort,nuc);
nuc = 'rLatVent';
subcort = 'aseg_rLatVent.asc';
subcortFs2mlab(subcort,nuc);
subcort = 'aseg_rInfLatVent.asc';
nuc = 'rInfLatVent';
subcortFs2mlab(subcort,nuc);