#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)
