# copy ponsnormd to pvc directory
cponsnormd = bg.copy_file(ponsnormd, pvcdir)
# get raparc
corgdir = os.path.join(pth, 'coreg_mri2fdg')
globstr = '%s/rB*aparc_aseg.nii'%(corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping '%(globstr))
continue
#copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
wm,gm,pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix='wm_')
gmf = pp.fname_presuffix(craparc, prefix='gm_')
pibif = pp.fname_presuffix(craparc, prefix='pibindex_')
aff = rousset.ni.load(craparc).get_affine()
rousset.to_file(wm, aff, wmf)
rousset.to_file(gm, aff, gmf)
rousset.to_file(pibi, aff, pibif)
rois = [gmf, wmf, pibif]
rsfs = rousset.compute_rsf(rois)
transfer_mtx = rousset.gen_transfer_matrix(rsfs, rois)
obs = rousset.get_observed_conc(cponsnormd, rois)
transferf = os.path.join(pvcdir, 'transfer_matrix')
rousset.np.save(transferf, transfer_mtx)
obsf = os.path.join(pvcdir, 'observed')
rousset.np.save(obsf, obs)
logging.info('Created %s'%(pvcdir))
continue
# copy ponsnormd to pvc directory
cponsnormd = bg.copy_file(ponsnormd, pvcdir)
# get raparc
corgdir = os.path.join(pth, 'coreg_mri2fdg')
globstr = '%s/rB*aparc_aseg.nii' % (corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error('%s missing, skipping ' % (globstr))
continue
#copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
wm, gm, pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix='wm_')
gmf = pp.fname_presuffix(craparc, prefix='gm_')
pibif = pp.fname_presuffix(craparc, prefix='pibindex_')
aff = rousset.ni.load(craparc).get_affine()
rousset.to_file(wm, aff, wmf)
rousset.to_file(gm, aff, gmf)
rousset.to_file(pibi, aff, pibif)
rois = [gmf, wmf, pibif]
rsfs = rousset.compute_rsf(rois)
transfer_mtx = rousset.gen_transfer_matrix(rsfs, rois)
obs = rousset.get_observed_conc(cponsnormd, rois)
transferf = os.path.join(pvcdir, 'transfer_matrix')
rousset.np.save(transferf, transfer_mtx)
obsf = os.path.join(pvcdir, 'observed')
rousset.np.save(obsf, obs)
logging.info('Created %s' % (pvcdir))
continue
# copy dvr to pvc directory
cdvr = bg.copy_file(dvr, pvcdir)
# get raparc
corgdir = os.path.join(pth, "coreg")
globstr = "%s/rB*aparc_aseg.nii" % (corgdir)
raparc = pp.find_single_file(globstr)
if raparc is None:
logging.error("%s missing, skipping " % (globstr))
continue
# copy raparc_aseg to pvd dir
craparc = bg.copy_file(raparc, pvcdir)
# make brainamsk
wm, gm, pibi = rousset.generate_pibindex_rois_fs(craparc)
wmf = pp.fname_presuffix(craparc, prefix="wm_")
gmf = pp.fname_presuffix(craparc, prefix="gm_")
pibif = pp.fname_presuffix(craparc, prefix="pibindex_")
aff = rousset.ni.load(craparc).get_affine()
rousset.to_file(wm, aff, wmf)
rousset.to_file(gm, aff, gmf)
rousset.to_file(pibi, aff, pibif)
rois = [gmf, wmf, pibif]
rsfs = rousset.compute_rsf(rois)
transfer_mtx = rousset.gen_transfer_matrix(rsfs, rois)
obs = rousset.get_observed_conc(cdvr, rois)
transferf = os.path.join(pvcdir, "transfer_matrix")
rousset.np.save(transferf, transfer_mtx)
obsf = os.path.join(pvcdir, "observed")
rousset.np.save(obsf, obs)
logging.info("Created %s" % (pvcdir))
