def compute_rsf(rois):
""" computes an RSF for each roi in input argument and returns an array with same size as input """
sameshape, shape = check_roi_shape(rois)
if not sameshape:
raise AssertionError('ROIs do NOT have same shape, exiting program,'\
'check your ROIS dimensions')
startdir = os.getcwd()
fullshape = tuple([len(rois)] + list(shape))
rsfs = np.zeros(fullshape)
for ind, roi in enumerate(rois):
petpsf = es.PetPsf(roi)
xyresult = petpsf.convolve_xy()
zresult = petpsf.convolve_z()
file = petpsf.save_result()
sfile = pp.fname_presuffix(file, prefix='s')
smfile = metzler.smooth_mask_nipy(file, sfile, fwhm=4)
smdata = smfile.get_data()
rsfs[ind, :, :, :] = smdata
return rsfs
def compute_rsf(rois):
""" computes an RSF for each roi in input argument and returns an array with same size as input """
sameshape, shape = check_roi_shape(rois)
if not sameshape:
raise AssertionError('ROIs do NOT have same shape, exiting program,'\
'check your ROIS dimensions')
startdir = os.getcwd()
fullshape = tuple([len(rois)] + list(shape))
rsfs = np.zeros(fullshape)
for ind, roi in enumerate(rois):
petpsf = es.PetPsf(roi)
xyresult = petpsf.convolve_xy()
zresult = petpsf.convolve_z()
file = petpsf.save_result()
sfile = pp.fname_presuffix(file, prefix='s')
smfile = metzler.smooth_mask_nipy(file,sfile,fwhm=4)
smdata = smfile.get_data()
rsfs[ind,:,:,:] = smdata
return rsfs
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
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))
return obs_conc
def calc_pvc_values(transfer_mtx, observed):
corrected = np.matrix(np.linalg.inv(transfer_mtx))* \
np.transpose(np.matrix(observed))
return corrected
if __name__ == '__main__':
testdir = os.path.abspath('../test')
aparc_aseg = os.path.join(testdir, 'rB09-230_v1_aparc_aseg.nii')
dvr = os.path.join(testdir, 'DVR-B09-230_v1_2012-06-08-15-07.nii.gz')
wm = mask_from_aseg(aparc_aseg, wm_aseg())
gm = mask_from_aseg(aparc_aseg, gm_aseg())
pibi = mask_from_aseg(aparc_aseg, pibindex_aseg())
wm, gm, pibi = generate_pibindex_rois_fs(aparc_aseg)
wmf = pp.fname_presuffix(aparc_aseg, prefix='wm_')
gmf = pp.fname_presuffix(aparc_aseg, prefix='gm_')
pibif = pp.fname_presuffix(aparc_aseg, prefix='pibindex_')
aff = ni.load(aparc_aseg).get_affine()
to_file(wm, aff, wmf)
to_file(gm, aff, gmf)
to_file(pibi, aff, pibif)
rois = [gmf, wmf, pibif]
rsfs = compute_rsf(rois)
transfer_mtx = gen_transfer_matrix(rsfs, rois)
obs = get_observed_conc(dvr, rois)
correct = calc_pvc_values(transfer_mtx, obs)
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
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))
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))
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))
mask = np.logical_and(roidat > 0, petdat > 0)
obs_conc[jval] = petdat[mask].mean()
return obs_conc
def calc_pvc_values(transfer_mtx, observed):
corrected = np.matrix(np.linalg.inv(transfer_mtx))* \
np.transpose(np.matrix(observed))
return corrected
if __name__ == '__main__':
testdir = os.path.abspath('../test')
aparc_aseg = os.path.join(testdir, 'rB09-230_v1_aparc_aseg.nii')
dvr = os.path.join(testdir,'DVR-B09-230_v1_2012-06-08-15-07.nii.gz')
wm = mask_from_aseg(aparc_aseg, wm_aseg())
gm = mask_from_aseg(aparc_aseg, gm_aseg())
pibi = mask_from_aseg(aparc_aseg, pibindex_aseg())
wm,gm,pibi = generate_pibindex_rois_fs(aparc_aseg)
wmf = pp.fname_presuffix(aparc_aseg, prefix='wm_')
gmf = pp.fname_presuffix(aparc_aseg, prefix='gm_')
pibif = pp.fname_presuffix(aparc_aseg, prefix='pibindex_')
aff = ni.load(aparc_aseg).get_affine()
to_file(wm, aff, wmf)
to_file(gm, aff, gmf)
to_file(pibi, aff, pibif)
rois = [gmf, wmf, pibif]
rsfs = compute_rsf(rois)
transfer_mtx = gen_transfer_matrix(rsfs, rois)
obs = get_observed_conc(dvr, rois)
correct = calc_pvc_values(transfer_mtx, obs)
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
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))
