import io_meld as io
import os
#parse commandline arguments pointing to subject_dir etc
parser = argparse.ArgumentParser(description='filter intrinsic curvature')
parser.add_argument('subject_dir', type=str, help='path to subject dir')
parser.add_argument('subject_ids',
type=str,
help='textfile containing list of subject ids')
args = parser.parse_args()
#save subjects dir and subject ids. import the text file containing subject ids
subject_dir = args.subject_dir
subject_ids_filename = args.subject_ids
subject_ids = np.loadtxt(subject_dir + subject_ids_filename, dtype='str')
hemis = ['lh', 'rh']
for h in hemis:
for s in subject_ids:
if not os.path.isfile(subject_dir + s + '/xhemi/surf_meld/' + h +
'.pial.K_filtered.mgh'):
demo = nb.load(subject_dir + s + '/surf_meld/' + h + '.pial.K.mgh')
curvature = io.load_mgh(subject_dir + s + '/surf_meld/' + h +
'.pial.K.mgh')
curvature = np.absolute(curvature)
io.save_mgh(
subject_dir + s + '/surf_meld/' + h + '.pial.K_filtered.mgh',
curvature, demo)
subject_ids=np.loadtxt(subject_dir+subject_ids_filename, dtype='str')
measures=['.thickness_z_on_lh.sm10.mgh', '.asym.thickness_z.sm10.mgh',
'.w-g.pct_z_on_lh.sm10.mgh','.asym.w-g.pct_z.sm10.mgh',
'.pial.K_filtered_2_z_on_lh.sm20.mgh','.asym.pial.K_filtered_2_z.sm20.mgh',
'.curv_on_lh.mgh','.sulc_on_lh.mgh',
'.gm_FLAIR_0.75_z_on_lh.sm10.mgh','.gm_FLAIR_0.5_z_on_lh.sm10.mgh',
'.gm_FLAIR_0.25_z_on_lh.sm10.mgh','.gm_FLAIR_0_z_on_lh.sm10.mgh',
'.wm_FLAIR_0.5_z_on_lh.sm10.mgh','.wm_FLAIR_1_z_on_lh.sm10.mgh',
'.asym.gm_FLAIR_0.75_z.sm10.mgh','.asym.gm_FLAIR_0.5_z.sm10.mgh',
'.asym.gm_FLAIR_0.25_z.sm10.mgh','.asym.gm_FLAIR_0_z.sm10.mgh',
'.asym.wm_FLAIR_0.5_z.sm10.mgh','.asym.wm_FLAIR_1_z.sm10.mgh']
hemis=['lh','rh']
demo=nb.load(subject_dir+subject_ids[0]+'/xhemi/surf/'+hemis[0]+measures[0])
for h in hemis:
for m in measures:
control_data=np.zeros((len(subject_ids),len(demo.get_data())))
k=-1
for s in subject_ids:
k+=1
control_data[k]=io.import_mgh(subject_dir+s+'/xhemi/surf/'+h+m)
mean=np.mean(control_data,axis=0)
std=np.std(control_data,axis=0)
io.save_mgh(subject_dir+'template_control/'+h+'.mu'+m,mean,demo)
io.save_mgh(subject_dir+'template_control/'+h+'.std'+m,mean,demo)
#save subjects dir and subject ids. import the text file containing subject ids
subject_dir=args.subject_dir
subject_ids_filename=args.subject_ids
subject_ids=np.loadtxt(subject_dir+subject_ids_filename, dtype='str')
measures=['.thickness_z_on_lh.sm10.mgh', '.asym.thickness_z.sm10.mgh',
'.w-g.pct_z_on_lh.sm10.mgh','.asym.w-g.pct_z.sm10.mgh',
'.pial.K_filtered_2_z_on_lh.sm20.mgh','.asym.pial.K_filtered_2_z.sm20.mgh',
'.curv_on_lh.mgh','.sulc_on_lh.mgh',
'.gm_FLAIR_0.75_z_on_lh.sm10.mgh','.gm_FLAIR_0.5_z_on_lh.sm10.mgh',
'.gm_FLAIR_0.25_z_on_lh.sm10.mgh','.gm_FLAIR_0_z_on_lh.sm10.mgh',
'.wm_FLAIR_0.5_z_on_lh.sm10.mgh','.wm_FLAIR_1_z_on_lh.sm10.mgh',
'.asym.gm_FLAIR_0.75_z.sm10.mgh','.asym.gm_FLAIR_0.5_z.sm10.mgh',
'.asym.gm_FLAIR_0.25_z.sm10.mgh','.asym.gm_FLAIR_0_z.sm10.mgh',
'.asym.wm_FLAIR_0.5_z.sm10.mgh','.asym.wm_FLAIR_1_z.sm10.mgh']
hemis=['lh','rh']
demo=nb.load(subject_dir+subject_ids[0]+'/xhemi/surf/'+hemis[0]+measures[0])
for h in hemis:
for m in measures:
control_mu=io.load_mgh('template_control/'+h+'.mu'+m)
control_std=io.load_mgh('template_control/'+h+'.std'+m)
for s in subject_ids:
subject_measure=io.load_mgh(subject_dir+s+'/xhemi/surf/'+h+m)
z_measure=(subject_measure-control_mu)/control_std)
io.save_mgh(subject_dir+s+'/xhemi/surf/'+h+'inter_z.'+m,z_measure,demo)
)
break
print("Creating T1 control means and stds")
for h in hemis:
for m in measures:
control_data = np.zeros(
(len(control_subjects), len(demo.get_data())))
k = -1
for s in control_subjects:
k += 1
control_data[k] = io.import_mgh(subject_dir + s +
'/xhemi/surf_meld/' + h + m)
mean = np.mean(control_data, axis=0)
std = np.std(control_data, axis=0)
io.save_mgh(os.path.join(control_dir, f, h + '.mu' + m), mean,
demo)
io.save_mgh(os.path.join(control_dir, f, h + '.std' + m), std,
demo)
#count how many FLAIR controls
flair_controls = []
for fs_id in control_subjects:
if os.path.isfile(
subject_dir + fs_id +
'/xhemi/surf_meld/lh.on_lh.intra_z.gm_FLAIR_0.75.sm10.mgh'):
flair_controls.append(fs_id)
if len(flair_controls) < 20:
print(
"Found " + str(len(flair_controls)) +
" FLAIR controls. As this is less than 20, we will use MELD template FLAIR controls for normalisation step"
for h in hemis:
for s in subject_ids:
demo = nb.load(
os.path.join(subject_dir, s, 'surf_meld', h + measures[0]))
cortex = nb.freesurfer.io.read_label(
os.path.join(subject_dir, s, 'label', h + '.cortex.label'))
for m in measures:
if not os.path.isfile(
os.path.join(subject_dir, s, 'surf_meld',
h + '.intra_z' + m)):
subject_measure = io.load_mgh(
os.path.join(subject_dir, s, 'surf_meld', h + m))
z_measure = (subject_measure - np.mean(
subject_measure[cortex])) / np.std(subject_measure[cortex])
io.save_mgh(
os.path.join(subject_dir, s, 'surf_meld',
h + '.intra_z' + m), z_measure, demo)
#only do FLAIR measures if present
if os.path.isfile(
os.path.join(subject_dir, s, 'surf_meld',
h + flair_measures[0])):
for m in flair_measures:
if not os.path.isfile(
os.path.join(subject_dir, s, 'surf_meld',
h + '.intra_z' + m)):
subject_measure = io.load_mgh(
os.path.join(subject_dir, s, 'surf_meld', h + m))
z_measure = (subject_measure -
np.mean(subject_measure[cortex])) / np.std(
subject_measure[cortex])
io.save_mgh(
elif '15T' in fs_id:
f='15T'
if os.path.isfile(subject_dir + fs_id + '/xhemi/surf_meld/lh.on_lh.intra_z.gm_FLAIR_0.75.sm10.mgh'):
measures=['.on_lh.intra_z.thickness.sm10.mgh', '.asym.on_lh.intra_z.thickness.sm10.mgh',
'.on_lh.intra_z.w-g.pct.sm10.mgh','.asym.on_lh.intra_z.w-g.pct.sm10.mgh',
'.on_lh.intra_z.pial.K_filtered.sm20.mgh','.asym.on_lh.intra_z.pial.K_filtered.sm20.mgh',
'.on_lh.curv.mgh','.on_lh.sulc.mgh',
'.asym.on_lh.curv.mgh','.asym.on_lh.sulc.mgh',
'.on_lh.intra_z.gm_FLAIR_0.75.sm10.mgh','.on_lh.intra_z.gm_FLAIR_0.5.sm10.mgh',
'.on_lh.intra_z.gm_FLAIR_0.25.sm10.mgh','.on_lh.intra_z.gm_FLAIR_0.sm10.mgh',
'.on_lh.intra_z.wm_FLAIR_0.5.sm10.mgh','.on_lh.intra_z.wm_FLAIR_1.sm10.mgh',
'.asym.on_lh.intra_z.gm_FLAIR_0.75.sm10.mgh','.asym.on_lh.intra_z.gm_FLAIR_0.5.sm10.mgh',
'.asym.on_lh.intra_z.gm_FLAIR_0.25.sm10.mgh','.asym.on_lh.intra_z.gm_FLAIR_0.sm10.mgh',
'.asym.on_lh.intra_z.wm_FLAIR_0.5.sm10.mgh','.asym.on_lh.intra_z.wm_FLAIR_1.sm10.mgh']
else:
measures=['.on_lh.intra_z.thickness.sm10.mgh', '.asym.on_lh.intra_z.thickness.sm10.mgh',
'.on_lh.intra_z.w-g.pct.sm10.mgh','.asym.on_lh.intra_z.w-g.pct.sm10.mgh',
'.on_lh.intra_z.pial.K_filtered.sm20.mgh','.asym.on_lh.intra_z.pial.K_filtered.sm20.mgh',
'.on_lh.curv.mgh','.on_lh.sulc.mgh',
'.asym.on_lh.curv.mgh','.asym.on_lh.sulc.mgh']
demo=nb.load(subject_dir+fs_id+'/xhemi/surf_meld/'+hemis[0]+measures[0])
for h in hemis:
for m in measures:
control_mu=io.load_mgh(os.path.join(control_dir,f,h+'.mu'+m))
control_std=io.load_mgh(os.path.join(control_dir,f,h+'.std'+m))
subject_measure=io.load_mgh(subject_dir+fs_id+'/xhemi/surf_meld/'+h+m)
z_measure=np.divide((subject_measure-control_mu),control_std,out=np.zeros_like(subject_measure), where=control_std!=0)
io.save_mgh(subject_dir+fs_id+'/xhemi/surf_meld/'+h+'.inter_z'+m,z_measure,demo)