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
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))
