pvcdir, exists = bg.make_dir(pth, 'pvc_metzler')
if exists:
logging.error('%s exists, remove to re-run' % (pvcdir))
continue
# get ponsnormd
globstr = '%s/nonan-ponsnormed_%s*nii*' % (pth, subid)
ponsnormd = pp.find_single_file(globstr)
if ponsnormd is None:
logging.error('%s missing, skipping' % (globstr))
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
bmask = metzler.make_aseg_brainmask(craparc)
os.unlink(craparc)
smooth_bmask = pp.fname_presuffix(bmask, prefix='s')
_ = metzler.smooth_mask_nipy(bmask, smooth_bmask)
ero_bmask = metzler.fsl_erode2d(bmask)
pvcpet = metzler.calc_pvc(cponsnormd, ero_bmask, smooth_bmask)
os.unlink(cponsnormd)
logging.info('Created %s' % (pvcpet))
pvcdir, exists = bg.make_dir(dvrdir, 'pvc_metzler')
if exists:
logging.error('%s exists, remove to re-run' % (pvcdir))
continue
# get dvr
globstr = '%s/DVR-%s*nii*' % (dvrdir, subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error('%s missing, skipping' % (globstr))
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
bmask = metzler.make_aseg_brainmask(craparc)
os.unlink(craparc)
smooth_bmask = pp.fname_presuffix(bmask, prefix='s')
_ = metzler.smooth_mask_nipy(bmask, smooth_bmask)
ero_bmask = metzler.fsl_erode2d(bmask)
pvcpet = metzler.calc_pvc(cdvr, ero_bmask, smooth_bmask)
os.unlink(cdvr)
logging.info('Created %s' % (pvcpet))
if exists:
logging.error('%s exists, remove to re-run'%(pvcdir))
continue
# get ponsnormd
globstr = '%s/nonan-ponsnormed_%s*nii*'%(pth,subid)
ponsnormd = pp.find_single_file(globstr)
if ponsnormd is None:
logging.error('%s missing, skipping'%(globstr))
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
bmask = metzler.make_aseg_brainmask(craparc)
os.unlink(craparc)
smooth_bmask = pp.fname_presuffix(bmask, prefix='s')
_ = metzler.smooth_mask_nipy(bmask, smooth_bmask)
ero_bmask = metzler.fsl_erode2d(bmask)
pvcpet = metzler.calc_pvc(cponsnormd, ero_bmask, smooth_bmask)
os.unlink(cponsnormd)
logging.info('Created %s'%(pvcpet))
pvcdir, exists = bg.make_dir(dvrdir, "pvc_metzler")
if exists:
logging.error("%s exists, remove to re-run" % (pvcdir))
continue
# get dvr
globstr = "%s/DVR-%s*nii*" % (dvrdir, subid)
dvr = pp.find_single_file(globstr)
if dvr is None:
logging.error("%s missing, skipping" % (globstr))
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
bmask = metzler.make_aseg_brainmask(craparc)
os.unlink(craparc)
smooth_bmask = pp.fname_presuffix(bmask, prefix="s")
_ = metzler.smooth_mask_nipy(bmask, smooth_bmask)
ero_bmask = metzler.fsl_erode2d(bmask)
pvcpet = metzler.calc_pvc(cdvr, ero_bmask, smooth_bmask)
os.unlink(cdvr)
logging.info("Created %s" % (pvcpet))