#studies=['ds001','ds002'] # load the atlas atlasfile='/work/01329/poldrack/software_lonestar/atlases/sc_HO_atlas.nii.gz' atlasimg=nib.load(atlasfile) atlasdata=atlasimg.get_data() try: activation_data.has_key('foo') except: activation_data={} taskctr=0 tasklabels=[] for s in studies: activation_data[s]={} print s condkey=ofu.load_condkey(basedir+s+'/models/model001/condition_key.txt') for task in condkey.keys(): taskctr+=1 tasklabels.append(s+'_%d'%task) activation_data[s][task]={} groupbase=os.path.join(basedir,s,'group/model001/task%03d'%task) groupbase_list=os.listdir(groupbase) gfeat_list=[x for x in groupbase_list if x.find('.gfeat')>0] for gfeat in gfeat_list: gfeatdir=os.path.join(groupbase,gfeat) featnum=int(gfeat[4:7]) # print gfeatdir thresh_zstat_file=os.path.join(gfeatdir,'cope1.feat/thresh_zstat1.nii.gz') zstatimg=nib.load(thresh_zstat_file) zstatdata=zstatimg.get_data() activation_data[s][task][featnum]=get_atlas_activation(zstatdata,atlasdata)
assert os.path.exists(infile) assert os.path.exists(os.path.dirname(outfile)) behav=numpy.loadtxt(infile,skiprows=1) varnames=[i for i in open(infile).readline().strip().split()] print varnames newdirnames=['functional','anatomy','behav','model'] # fieldnamp and diffusion do not exist for ds007 so don't generate them basedir='/Users/poldrack/Dropbox/code/openfmri/nidm/ds007' newdir=basedir+'_new' if not os.path.exists(newdir): os.mkdir(newdir) logmsg('mkdir %s'%newdir) condkey=load_condkey(os.path.join(basedir,'models/model001/condition_key.txt')) subdirs=glob.glob(os.path.join(basedir,'sub*')) for subdir in subdirs: try: assert os.path.exists(os.path.join(subdir,'BOLD')) assert os.path.exists(os.path.join(subdir,'anatomy')) except: print subdir,'does not appear to be a good subject dir' continue subcode=subdir.split('/')[-1] newsubdir=os.path.join(newdir,subcode) if not os.path.exists(newsubdir): os.mkdir(newsubdir)
assert os.path.exists(os.path.dirname(outfile)) behav = numpy.loadtxt(infile, skiprows=1) varnames = [i for i in open(infile).readline().strip().split()] print varnames newdirnames = ['functional', 'anatomy', 'behav', 'model'] # fieldnamp and diffusion do not exist for ds007 so don't generate them basedir = '/Users/poldrack/Dropbox/code/openfmri/nidm/ds007' newdir = basedir + '_new' if not os.path.exists(newdir): os.mkdir(newdir) logmsg('mkdir %s' % newdir) condkey = load_condkey( os.path.join(basedir, 'models/model001/condition_key.txt')) subdirs = glob.glob(os.path.join(basedir, 'sub*')) for subdir in subdirs: try: assert os.path.exists(os.path.join(subdir, 'BOLD')) assert os.path.exists(os.path.join(subdir, 'anatomy')) except: print subdir, 'does not appear to be a good subject dir' continue subcode = subdir.split('/')[-1] newsubdir = os.path.join(newdir, subcode) if not os.path.exists(newsubdir): os.mkdir(newsubdir)