"""
Get the values as mask
from the neurosynth result
"""
lg = setLog._log(self.logf)
lg.info('Doing mask_neurosynth_file')
cmd = split("3dcalc -a %s -expr 'step(a)' \
-prefix %s " % (self.input, outfile))
lg.info("Command: \n%s" % cmd)
p = subprocess.run(cmd, stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
lg.info(p.stdout.decode("utf-8", "strict"))
lg.info("Done with mask_neurosynth_file")
if __name__ == '__main__':
workdir = os.path.join('/Users/andric/Documents/workspace',
'AVPPI', 'nii', 'group_effects_dec')
ns_masks = ['lateral_occipital_pFgA_z_FDR_0.01', 'mt_pFgA_z_FDR_0.01']
logs = os.path.join(workdir, 'mask_to_surface')
for f in ns_masks:
ms = mask_to_surface(os.path.join(workdir, '%s.nii.gz' % f), logs)
outmask = os.path.join(workdir, 'stepmask_%s' % f)
ms.mask_neurosynth_file(outmask)
pn = 1.0
for hemi in ['lh', 'rh']:
outname = '%s_%s_pn%s_MNI_N27.1D' % (outmask, hemi, pn)
pr.vol2surf_mni(workdir, 'max_abs', hemi,
'%s+tlrc' % outmask, pn, outname, logs, local=True)
@author: andric
"""
import os
import procs as pr
if __name__ == '__main__':
effects = ['Aentr', 'Ventr', 'Aentr_intxn']
pn_list = ['1.0', '2.0']
mapping = 'max_abs'
for block in [20, 15, 10]:
outdir = os.path.join(os.environ['avp'], 'nii', 'group_effects_%sblk' % block)
logf = os.path.join(outdir, 'project_to_surf')
for ef in effects:
if os.path.exists(os.path.join(os.environ['avp'], 'nii',
'group_effects_%sblk' % block,
'clust_%s_flt2_%sblk_msk_mema_mask+tlrc.BRIK.gz' % (ef, block))):
parent_pref = os.path.join(outdir, 'clust_%s_flt2_%sblk_msk_mema' % (ef, block))
for hemi in ['lh', 'rh']:
outname = '%s_%s_no_pn_MNI_N27.1D' % (parent_pref, hemi)
pr.vol2surf_mni_no_pn(outdir, mapping, hemi,
'%s+tlrc' % parent_pref, outname, logf)
for pn in pn_list:
outname = '%s_%s_pn%s_MNI_N27.1D' % (parent_pref, hemi, pn)
pr.vol2surf_mni(outdir, mapping, hemi,
'%s+tlrc' % parent_pref, pn, outname, logf)
