else:
raise OSError('%s exists, remove to re-run'%outdir)
# Split files of each subject containing all ic's
infiles = glob(subic_globstr)
for subfile in infiles:
subid = pydr.get_subid(subfile, pattern=subid_pattern)
allic = pydr.split_components(subfile, subid, outdir)
# Merge files of each ic across subjects
for cn, item in enumerate(allic): #Search through ics using last subject's output
datadir, ic = os.path.split(item)
subid = pydr.get_subid(item, pattern=subid_pattern)
globstr = ic.replace(subid, '*')
mergefile, subject_order = pydr.merge_components(datadir,
globstr = globstr,
subid_pattern = subid_pattern)
outfile = os.path.join(outdir, 'subject_order_ic%04d'%cn)
with open(outfile, 'w+') as fid:
fid.write('\n'.join(subject_order)) #Write out subject order for each ic
# Rename files with ic count starting at 1 and unzip
for cn, item in enumerate(glob(ic4d_globstr)):
datadir, filename = os.path.split(item)
new_cn = cn + 1
newfile = os.path.join(datadir, ''.join(['ic','%03d'%new_cn, '_4D.nii.gz']))
os.rename(item, newfile)
cmd = CommandLine('gunzip %s'%(newfile))
cmd.run()
order_file = os.path.join(datadir, 'subject_order_ic%04d'%cn)
new_order_file = os.path.join(datadir, 'subject_order_ic%03d'%new_cn)
subid,
'func',
'confound_regressors_6mm.txt') #Name of confound file
## If you want residuals to be output, change out_res to True below
stage2_ts, stage2_tsz = pydr.sub_spatial_map(tmpf, txtf, mask, outdir,
desnorm=True, out_res=True,mvt=mvtfile)
subd.update({subid:stage2_ts})
###Split subject 4d file into separate 3d files for each component
allic = pydr.split_components(stage2_ts, subid, outdir)
###Concat ics across subjects.
###Only merges ICs from gica,
###not those of confound regressors
###############################################
for cn, item in enumerate(allic[:num_ics]): #Search through ics using last subject's output
datadir, ic = os.path.split(item)
subid = pydr.get_subid(item)
globstr = ic.replace(subid, '*')
mergefile, subject_order = pydr.merge_components(datadir,
globstr = globstr)
outfile = os.path.join(outdir, 'subject_order_ic%04d'%cn)
with open(outfile, 'w+') as fid:
fid.write('\n'.join(subject_order)) #Write out subject order for each ic
os.chdir(startdir)