Closed carlottasabate closed 2 years ago
carlottasabate
commented
2 years ago call_bashhelper:
if [[ ${3} == 'brain' ]]; then
echo "Turning off bias/intensity correction & sanlm-filtering"
bias_reg=0
bias_fhwm="Inf"
app=0
sanlm=0
else
bias_reg=0.001
bias_fhwm=60
app=2
sanlm=2
fi#!/usr/bin/env python
import sys, getopt
import os
from nilearn import image
from scipy import ndimage
import pathlib
import nibabel as nb
import warnings
warnings.filterwarnings("ignore")
opj = os.path.join
def main(argv):
"""
---------------------------------------------------------------------------------------------------
call_gdhmasking
This script masks the input T1w-image according to the method from Gilles. You can find the
original at https://github.com/VU-Cog-Sci/mp2rage_preprocessing/blob/master/analysis/mask_mp2rage.py.
One thing was added: sometimes the bias field correction of the INV-2 images is not too good, resul-
ting in a bad brain extraction. To overcome this issue, you can re-run brain extraction on the non-
bias field corrected T1w-image (output from pymp2rage) with CAT12. This is a little more robust
against these issues. This is done with call_cat12, and the output is a brainmask in the manual_
masks directory called 'desc-mask_T1w.nii.gz'. The script will include this if it exists.
Args:
-s (--subj) subject number
-n (--ses) session number
-i (--inv=) second inversion image
-t (--t1w=) T1-weighted image
-d (--masks=) Directory containing the following masks:
- Dura mask '_desc-duramask'
- T1w mask '_desc-bet_mask'
- Sinus mask '_desc_sagittalsinus'
-o (--output=) Output basename (leave empty to overwrite inputs = default). This
will cause the T1w-masked image to end up in the same folder as
the mask itself! Just leave it empty..
- masked T1w: suffixed with _masked.nii.gz
- mask: suffixed with _brainmask.nii.gz
Outputs
- masked T1w image
- brainmask
Example:
call_gdhmasking -s sub-001 -n 1 -i inv2.nii.gz -u T1w.nii.gz -d /dir/with/masks
Notes:
Need at least the subject number!
if left to empty, it will look by default for the following files:
inv2 > /data_home/<subject>/ses-<ses>/anat/inv2.nii.gz
t1w > /pymp2rage/<subject>/ses-<ses>/T1w.nii.gz
masks > /manual_masks/<subject>/ses-<ses>
---------------------------------------------------------------------------------------------------
"""
subject = None
ses = None
inv2 = None
t1w_fn = None
masks = None
output = None
try:
opts = getopt.getopt(argv,"hs:n:i:t:m:d:o:",["subj=", "ses=", "inv=", "t1w=", "masks=", "output="])[0]
except getopt.GetoptError:
print(main.__doc__)
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print(main.__doc__)
sys.exit()
elif opt in ("-s", "--subj"):
subject = arg
elif opt in ("-n", "--ses"):
ses = arg
elif opt in ("-i", "--inv"):
inv2 = arg
elif opt in ("-t", "--t1w"):
t1w_fn = arg
elif opt in ("-d", "--masks"):
masks = arg
elif opt in ("-o", "--output"):
output = arg
if len(argv) < 1:
print("\nNOT ENOUGH ARGUMENTS SPECIFIED")
print(main.__doc__)
sys.exit()
if subject == None:
raise ValueError("Need at the bare minimum at subject ID")
if ses == None:
sub_dir = subject
base = f"{subject}"
else:
sub_dir = opj(subject, f'ses-{ses}')
base = f"{subject}_ses-{ses}"
# This stuff will create some default options if they are left empty. It assumes that you have the variables
# from spinoza_setup available in your environment. If not, it will throw a key-error
if inv2 == None:
for f in os.listdir(opj(os.environ['DIR_DATA_HOME'], sub_dir, 'anat')):
if f.endswith("inv-2_part-mag.nii.gz"):
inv2 = opj(opj(os.environ['DIR_DATA_HOME'], sub_dir, 'anat', f))
if t1w_fn == None:
for f in os.listdir(opj(os.environ['PYMP2RAGE'], sub_dir)):
if f.endswith("acq-{data}_T1w.nii.gz".format(data=os.environ['DATA'].upper())):
t1w_fn = opj(opj(os.environ['PYMP2RAGE'], sub_dir, f))
if masks == None:
masks = opj(os.environ['MASKS'], sub_dir)
if output == None:
masked_out = opj(os.environ['DIR_DATA_DERIV'], 'masked_{}'.format(os.environ['DATA'].lower()), sub_dir, 'anat', "{s}_acq-{a}_desc-masked_T1w.nii.gz".format(s=base, a=os.environ['DATA']))
mask_out = opj(os.environ['MASKS'], sub_dir, "{s}_acq-{a}_desc-brainmask.nii.gz".format(s=base, a=os.environ['DATA']))
else:
masked_out = output + "masked_T1w.nii.gz"
mask_out = output + "brainmask.nii.gz"
# Start procedure
print("Starting procedure ..")
all_masks = {}
for j in os.listdir(masks):
for i in ['cat_dura', 'dura_orig', 'dura_dil', 'cat_mask', 'spm_mask', '-outside', 'sinus', 'inside']:
if i in j:
if os.environ['DATA'].upper() in j:
all_masks[i] = opj(masks, j)
# Check which masks we actually have
try:
dura_mask = all_masks['dura_dil'] # use the dilated dura by default
except:
try:
dura_mask = all_masks['cat_dura'] # if dilated doesn't exist, use the dura from CAT
except:
try:
all_masks['dura_orig'] # if THAT also doesn't exist, run spinoza_createskullduramasks
except:
print("Could not find any dura image. It's most like you don't have a T2w-image, so run spinoza_createskullduramasks (module 11)")
print("If you do have a T2-image, run spinoza_registration (module 6) and spinoza_sinusfrommni (module 7), to create a dura mask")
sys.exit(1)
dura_mask = None
try:
t1w_mask = all_masks['cat_mask']
except:
try:
t1w_mask = all_masks['gdh_mask']
except:
t1w_mask = None
try:
inv2_mask = all_masks['spm_mask']
except:
inv2_mask = None
try:
outside = all_masks['-outside']
except:
try:
outside = all_masks['sinus']
except:
raise ValueError("Could not find sinus mask")
try:
inside = all_masks['inside']
except:
inside = None
print("Loading in masks")
for i in [dura_mask, t1w_mask, outside, inside, inv2_mask]:
if i != None:
print(f" found: {i}")#.format(file=os.path.basename(i)))
print("Fetching structural files")
for i,t in zip([inv2, t1w_fn], ["inv2", "T1w"]):
if i != None:
print(f" found: {i}")#.format(file=os.path.basename(i)))
else:
print(f"Missing '{t}' files..")
if not os.path.exists(os.path.dirname(masked_out)):
pathlib.Path(os.path.dirname(masked_out)).mkdir(parents=True, exist_ok=True)
# print(" Remove ugly background noise")
if inside:
t1w_mask = image.math_img('(t1w_mask + inside) > 0',
t1w_mask=t1w_mask,
inside=inside)
if inv2_mask:
t1w_mask = image.math_img('(t1w_mask + inv2) > 0',
t1w_mask=t1w_mask,
inv2=inv2_mask)
# cat12 mask can be more robust against intensity issues
# if cat12:
# t1w_mask = image.math_img('(t1w_mask + cat12) > 0',
# t1w_mask=t1w_mask,
# cat12=cat12)
outside_fn = opj(masks, "{s}_acq-{a}_desc-outside.nii.gz".format(s=base, a=os.environ['DATA']))
if not "-outside" in outside:
print("Creating outside mask")
if not "dura_dil" in dura_mask:
# Dilate dura mask
dilated_dura_mask = ndimage.binary_dilation(image.load_img(dura_mask).get_fdata(),
iterations=2)
dilated_dura_mask = image.new_img_like(dura_mask, dilated_dura_mask)
# print(t1w_mask.affine)
# print(nb.load(dura_mask).affine)
# print(dilated_dura_mask.affine)
# Make a mask of dilated dura, but only outwards
dilated_dura_mask = image.math_img('(dilated_dura_mask - (t1w_mask - dura_mask)) > 0',
t1w_mask=t1w_mask,
dura_mask=dura_mask,
dilated_dura_mask=dilated_dura_mask)
if inside:
dilated_dura_mask = image.math_img('dilated_dura_mask - inside > 0',
dilated_dura_mask=dilated_dura_mask,
inside=inside)
dura_fn = opj(os.path.dirname(mask_out), "{s}_acq-{a}_desc-dura_dilated.nii.gz".format(s=base, a=os.environ['DATA']))
dilated_dura_mask.to_filename(dura_fn)
dura_mask = dura_fn
# Create one 'outside' mask consisting of dilated dura mask and sinus
outside = image.math_img('(dura + sinus) > 0',
dura=dura_mask,
sinus=outside)
# outside_fill = ndimage.morphology.binary_fill_holes(outside.get_fdata())
# print(type(outside_fill))
#
# outside = nb.Nifti1Image(outside_fill, affine=outside.affine, header=outside.header)
# print(type(outside))
# print(outside_fn)
outside.to_filename(outside_fn)
try:
print("Copying geometry from input T1w-image")
os.system(f"fslcpgeom {t1w_fn} {outside_fn}")
except:
print("WARNING: could not copy geometry from {} to {}".format(t1w_fn, outside_fn))
try:
print("Manually edit the outside mask in ITKSnap")
cmd_txt = "itksnap -g {anat} -s {dura}".format(anat=t1w_fn, dura=outside_fn)
os.system(cmd_txt)
except:
print("Could not initiate ITKsnap to manually edit outside mask")
# itksnap removes sform, resulting in problems with image.math_img. Copy qform2sform with fslorient
# os.system(f"call_resample {outside_fn} {t1w_fn}")
# Stuff like dura should be put to 0, not just multiplied with INV2
print("Set sagittal sinus and dura stuff to zero")
t1w = image.math_img('t1w * (np.ones_like(t1w) - outside)',
t1w=t1w_fn,
outside=outside_fn)
t1w_mask = image.math_img('t1w_mask - outside > 0',
t1w_mask=t1w_mask,
outside=outside_fn)
t1w_mask.to_filename(mask_out)
if inv2 != None:
new_t1w = image.math_img('t1w * t1w_mask * np.mean(inv2[t1w_mask == 1]/np.max(inv2))'
'+ t1w * inv2/np.max(inv2) * (1-t1w_mask)',
t1w=t1w,
t1w_mask=t1w_mask,
inv2=inv2)
new_t1w.to_filename(masked_out)
else:
t1w.to_filename(masked_out)
print("Masking procedure completed")
if __name__ == "__main__":
main(sys.argv[1:])
master:spinoza_averageanatomies:spinoza_brainextraction:spinoza_registration:spinoza_sinusfrommni: