Skip to content

Commit

Permalink
Correcting the white matter parcellation
Browse files Browse the repository at this point in the history
  • Loading branch information
Yasser Alemán Gómez committed Aug 20, 2024
1 parent 71947b0 commit 1d3abdd
Show file tree
Hide file tree
Showing 3 changed files with 102 additions and 134 deletions.
9 changes: 6 additions & 3 deletions MANIFEST.in
View file
Original file line number Diff line number Diff line change
Expand Up @@ -5,11 +5,14 @@ include LICENSE
include README.rst

recursive-include tests *
recursive-include chimera/data/ *.annot
recursive-include chimera/data/ *.nii.gz
recursive-include chimera/data/ *.gcs
recursive-include chimera/data/ *.tsv

recursive-exclude * __pycache__
recursive-exclude * *.py[co]

recursive-include docs *.rst conf.py Makefile make.bat *.jpg *.png *.gif

packages = ['.','data','config','docs'],

package_data={'data':['*'],'config':['*'],'docs':['*'],},
packages = ['.','data','config','docs'],
226 changes: 95 additions & 131 deletions chimera/chimera.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -193,9 +193,8 @@ def _prepare_templates(self, fssubj_dir:str = None):


# Detecting the base directory
cwd = os.path.dirname(os.path.abspath(__file__))
chim_dir = os.path.dirname(cwd)

chim_dir = os.path.dirname(os.path.abspath(__file__))

# Reading the names of the supra-regions
supra_names = list(self.parc_dict.keys())

Expand Down Expand Up @@ -281,14 +280,16 @@ def _prepare_templates(self, fssubj_dir:str = None):
atlas_ext = '.gcs'
method = 'gcs2indiv'



ctx_parc_lh = glob(os.path.join(atlas_dir, '*-L_*' + atlas_ext))
ctx_parc_rh = glob(os.path.join(atlas_dir, '*-R_*' + atlas_ext))

# Filtering for selecting the correct cortical parcellation
ctx_parc_lh = cltmisc._filter_by_substring(ctx_parc_lh, atlas_names, boolcase=False)
ctx_parc_rh = cltmisc._filter_by_substring(ctx_parc_rh, atlas_names, boolcase=False)

if not ctx_parc_lh_annot or not ctx_parc_rh_annot:
if not ctx_parc_lh or not ctx_parc_rh:
raise ValueError("Cortical parcellations should be supplied for both hemispheres.")

else:
Expand Down Expand Up @@ -741,11 +742,6 @@ def _build_parcellation1(self, t1:str, bids_dir:str,
chim_dir = Path(chim_dir)
chim_dir.mkdir(parents=True, exist_ok=True)

# Create the anat directory if it does not exist
tmp_dir = os.path.join(str(chim_dir), 'tmp')
tmp_dir = Path(tmp_dir)
tmp_dir.mkdir(parents=True, exist_ok=True)

######## ----------- Detecting FREESURFER_HOME directory ------------- #
fshome_dir = os.getenv('FREESURFER_HOME')
fslut_file = os.path.join(fshome_dir, 'FreeSurferColorLUT.txt')
Expand Down Expand Up @@ -1231,138 +1227,106 @@ def _build_parcellation1(self, t1:str, bids_dir:str,

## -------- Creating the volumetric parcellation ---------------
out_vol_dir = os.path.join(deriv_dir, self.parc_dict["Cortical"]["deriv_volfold"], path_cad)
if growwm is not None:
for ngrow in np.arange(len(growwm)):
if growwm[ngrow] == '0':
out_vol_name = fullid + '_' + at_name + '_dseg.nii.gz'
else:

ent_dict = cltbids._str2entity(at_name)
if 'desc' in ent_dict.keys():
ent_dict["desc"] = ent_dict["desc"] + 'grow' + str(growwm[ngrow]) + 'mm'
tmp_str = cltbids._entity2str(ent_dict)
out_vol_name = fullid + '_' + tmp_str + '_dseg.nii.gz'
else:
out_vol_name = fullid + '_' + at_name + '_desc-grow' + str(growwm[ngrow]) + 'mm_dseg.nii.gz'

sub2proc._surf2vol(atlas=at_name,
out_vol=os.path.join(out_vol_dir, out_vol_name),
gm_grow=growwm[ngrow],
bool_mixwm = bool_mixwm,
force=False, bool_native=True,
color_table=['tsv', 'lut'])

chim_parc_name = cltbids._replace_entity_value(out_vol_name, {"atlas": "chimera" + chim_code} )
chim_parc_file = os.path.join(str(chim_dir), chim_parc_name)
chim_parc_lut = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "lut"}))
chim_parc_tsv = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "tsv"}))
if growwm is None:
growwm = ['0']

for ngrow in np.arange(len(growwm)):
if growwm[ngrow] == '0':
out_vol_name = fullid + '_' + at_name + '_dseg.nii.gz'
else:

if not os.path.isfile(chim_parc_file) or not os.path.isfile(chim_parc_lut) or not os.path.isfile(chim_parc_tsv) or force:
# Creating the joined parcellation
ref_image = np.zeros_like(t1_image.get_fdata(), dtype=np.int32)
chim_parc = cltparc.Parcellation(parc_file=ref_image, affine=affine)

ctx_parc = cltparc.Parcellation(parc_file=os.path.join(out_vol_dir, out_vol_name))
ctx_parc._remove_by_name(names2remove=['unknown', 'medialwall', 'corpuscallosum'])

lh_ctx_parc = copy.deepcopy(ctx_parc)
rh_ctx_parc = copy.deepcopy(ctx_parc)

lh_ctx_parc._keep_by_name(names2look='ctx-lh-')
rh_ctx_parc._keep_by_name(names2look='ctx-rh-')

# Detect if wm is in the names
# tmp_brain = cltmisc._filter_by_substring(ctx_parc.name, 'wm-brain-')
# if tmp_brain:
# bool_wm = True
# brain_wm_parc = copy.deepcopy(ctx_parc)
# brain_wm_parc._keep_by_name(names2look=tmp_brain)
# brain_wm_parc._rearange_parc(offset=2999)
# else:
# bool_wm = False

tmp_lh = cltmisc._filter_by_substring(ctx_parc.name, 'wm-lh-')
if tmp_lh:
bool_wm = True
lh_wm_parc = copy.deepcopy(ctx_parc)
lh_wm_parc._keep_by_name(names2look=tmp_lh)

ent_dict = cltbids._str2entity(at_name)
if 'desc' in ent_dict.keys():
if bool_mixwm:
ent_dict["desc"] = ent_dict["desc"] + 'grow' + str(growwm[ngrow]) + 'mm+mixwm'
else:
bool_wm = False


tmp_rh = cltmisc._filter_by_substring(ctx_parc.name, 'wm-rh-')
if tmp_rh:
bool_wm = True
rh_wm_parc = copy.deepcopy(ctx_parc)
rh_wm_parc._keep_by_name(names2look=tmp_rh)
rh_wm_parc._rearange_parc(offset=3000)

ent_dict["desc"] = ent_dict["desc"] + 'grow' + str(growwm[ngrow]) + 'mm'
tmp_str = cltbids._entity2str(ent_dict)
out_vol_name = fullid + '_' + tmp_str + '_dseg.nii.gz'
else:
if bool_mixwm:
out_vol_name = fullid + '_' + at_name + '_desc-grow' + str(growwm[ngrow]) + 'mm+mixwm_dseg.nii.gz'
else:
bool_wm = False

rh_ctx_parc._rearange_parc()
chim_parc._add_parcellation(rh_ctx_parc, append=True)
if "rh_parc" in locals():
chim_parc._add_parcellation(rh_parc, append=True)

lh_ctx_parc._rearange_parc()
chim_parc._add_parcellation(lh_ctx_parc, append=True)
if "lh_parc" in locals():
chim_parc._add_parcellation(lh_parc, append=True)

if "mid_parc" in locals():
chim_parc._add_parcellation(mid_parc, append=True)

if bool_wm:
chim_parc._add_parcellation(rh_wm_parc, append=True, )

lh_wm_parc._rearange_parc(offset=3000 + rh_ctx_parc.maxlab + nrh_subc)
chim_parc._add_parcellation(lh_wm_parc, append=True)

chim_parc._save_parcellation(out_file=chim_parc_file, affine=affine, save_lut=True, save_tsv=True)
out_vol_name = fullid + '_' + at_name + '_desc-grow' + str(growwm[ngrow]) + 'mm_dseg.nii.gz'

else:
out_vol_name = fullid + '_' + at_name + '_dseg.nii.gz'
sub2proc._surf2vol(atlas=at_name,
out_vol=os.path.join(out_vol_dir, out_vol_name),
gm_grow=growwm[ngrow],
bool_mixwm = bool_mixwm,
force=force, bool_native=True)

ctx_parc = cltparc.Parcellation(parc_file=os.path.join(out_vol_dir, out_vol_name))

lh_ctx_parc = copy.deepcopy(ctx_parc)
rh_ctx_parc = copy.deepcopy(ctx_parc)

lh_ctx_parc._keep_by_name(names2look='ctx-lh-')
rh_ctx_parc._keep_by_name(names2look='ctx-rh-')

# Detect if wm is in the names
tmp_names = lh_ctx_parc.name
tmp_lh = cltmisc._filter_by_substring(tmp_names, 'wm-')
if tmp_lh:
bool_wm = True
lh_wm_parc = copy.deepcopy(ctx_parc)
lh_wm_parc._keep_by_name(names2look='wm-lh-')
else:
bool_wm = False

tmp_names = rh_ctx_parc.name
tmp_rh = cltmisc._filter_by_substring(tmp_names, 'wm-rh-')
if tmp_rh:
bool_wm = True
rh_wm_parc = copy.deepcopy(ctx_parc)
else:
bool_wm = False






force=False, bool_native=True,
color_table=['tsv', 'lut'])

chim_parc_name = cltbids._replace_entity_value(out_vol_name, {"atlas": "chimera" + chim_code} )
chim_parc_file = os.path.join(str(chim_dir), chim_parc_name)
chim_parc_lut = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "lut"}))
chim_parc_tsv = os.path.join(str(chim_dir), cltbids._replace_entity_value(chim_parc_name, {"extension": "tsv"}))

if not os.path.isfile(chim_parc_file) or not os.path.isfile(chim_parc_lut) or not os.path.isfile(chim_parc_tsv) or force:
# Creating the joined parcellation
ref_image = np.zeros_like(t1_image.get_fdata(), dtype=np.int32)
chim_parc = cltparc.Parcellation(parc_file=ref_image, affine=affine)

ctx_parc = cltparc.Parcellation(parc_file=os.path.join(out_vol_dir, out_vol_name))
ctx_parc._remove_by_name(names2remove=['unknown', 'medialwall', 'corpuscallosum'])

lh_ctx_parc = copy.deepcopy(ctx_parc)
rh_ctx_parc = copy.deepcopy(ctx_parc)

lh_ctx_parc._keep_by_name(names2look='ctx-lh-')
nlh_ctx = len(lh_ctx_parc.index)
rh_ctx_parc._keep_by_name(names2look='ctx-rh-')
nrh_ctx = len(rh_ctx_parc.index)

# Detect the global White Matter
brain_wm_parc = copy.deepcopy(ctx_parc)
brain_wm_parc._keep_by_code(codes2look=[2, 41, 5001, 5002, 250, 251, 252, 253, 254, 255, 7, 46])
ind = np.where(brain_wm_parc.data != 0)
brain_wm_parc.data[ind] = 1
brain_wm_parc.index = [1]
brain_wm_parc.name = ['wm-brain-whitematter']
brain_wm_parc.color = ['#ffffff']
brain_wm_parc._rearange_parc(offset=2999)

# White Matter for the Right Hemisphere
tmp_rh = cltmisc._filter_by_substring(ctx_parc.name, 'wm-rh-')
if tmp_rh:
bool_wm = True
rh_wm_parc = copy.deepcopy(ctx_parc)
rh_wm_parc._keep_by_name(names2look=tmp_rh)
rh_wm_parc._rearange_parc(offset=3000)

else:
bool_wm = False

# White Matter for the Left Hemisphere
tmp_lh = cltmisc._filter_by_substring(ctx_parc.name, 'wm-lh-')
if tmp_lh:
bool_wm = True
lh_wm_parc = copy.deepcopy(ctx_parc)
lh_wm_parc._keep_by_name(names2look=tmp_lh)
lh_wm_parc._rearange_parc(offset=3000 + nrh_ctx + nrh_subc)
else:
bool_wm = False

rh_ctx_parc._rearange_parc()
chim_parc._add_parcellation(rh_ctx_parc, append=True)
if "rh_parc" in locals():
chim_parc._add_parcellation(rh_parc, append=True)

lh_ctx_parc._rearange_parc()
chim_parc._add_parcellation(lh_ctx_parc, append=True)
if "lh_parc" in locals():
chim_parc._add_parcellation(lh_parc, append=True)

if "mid_parc" in locals():
chim_parc._add_parcellation(mid_parc, append=True)

if bool_wm:
chim_parc._add_parcellation(brain_wm_parc, append=False)
chim_parc._add_parcellation(rh_wm_parc, append=False)
chim_parc._add_parcellation(lh_wm_parc, append=False)

chim_parc._save_parcellation(out_file=chim_parc_file, affine=affine, save_lut=True, save_tsv=True)


# Loading the JSON file containing the available parcellations
Expand Down
1 change: 1 addition & 0 deletions setup.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@
include_package_data=True,
keywords='chimera',
name='chimera',
packages=find_packages(include=['chimera', 'chimera.*']),
package_data={'chimera' :['chimera/data/*','chimera/config/*']},
test_suite='tests',
tests_require=test_requirements,
Expand Down

0 comments on commit 1d3abdd

Please sign in to comment.