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Merge pull request #51 from DCAN-Labs/t2output
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Segmentations and Masks Output in T1-native and T2-native Space
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@audreymhoughton
audreymhoughton authored Jun 7, 2023
2 parents 94bdf45 + 78b849c commit ecf73ff
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Showing 2 changed files with 46 additions and 47 deletions.
83 changes: 41 additions & 42 deletions run.py
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Original file line number Diff line number Diff line change
Expand Up @@ -533,26 +533,18 @@ def read_from_tsv(j_args, logger, col_name, *sub_ses):
return desired_output

def get_col_value_from_tsv(j_args, logger, tsv_path, ID_col, col_name, sub_ses):
columns = {x: "str" for x in (col_name, ID_col)}

# Read in sessions.tsv
tsv_df = pd.read_csv(
tsv_path, delim_whitespace=True, index_col=ID_col ##, dtype=columns
tsv_path, delim_whitespace=True, index_col=ID_col
)

print(tsv_df)
print("subses: ",{sub_ses})
print("ID_col: ", ID_col)
print("ensure_prefixed: ", ensure_prefixed(sub_ses[1], "ses-") if ID_col == "session_id" else ensure_prefixed(sub_ses[0], "sub-"))
print("tsv_df.shape: ", tsv_df.shape)
print("tsv_df.columns: ", tsv_df.columns)

# Get and return the col_name value from sessions.tsv

subj_row = tsv_df.loc[
ensure_prefixed(sub_ses[1], "ses-") if ID_col == "session_id" else ensure_prefixed(sub_ses[0], "sub-")
] # select where "participant_id" matches
if j_args["common"]["verbose"]:
logger.info(f"ID_col used to get details from tsv: {ID_col}")
logger.info(f"Subject details from tsv row:\n{subj_row}")
return int(subj_row[col_name])

Expand Down Expand Up @@ -797,23 +789,27 @@ def run_postBIBSnet(j_args, logger):
left_right_mask_nifti_fpath
)
logger.info("Finished dilating left/right segmentation mask")
nii_outfpath = correct_chirality_revert_to_native(dilated_LRmask_fpath,
nifti_file_paths, chiral_out_dir, xfm_ref_img_dict = run_correct_chirality(dilated_LRmask_fpath,
j_args, logger)
chiral_out_dir = os.path.dirname(nii_outfpath)
logger.info("The BIBSnet segmentation has had its chirality checked and "
"registered if needed. Now making aseg-derived mask.")

# TODO Skip mask creation if outputs already exist and not j_args[common][overwrite]
aseg_mask = make_asegderived_mask(j_args, chiral_out_dir, nii_outfpath) # NOTE Mask must be in native T1 space too
logger.info("A mask of the BIBSnet segmentation has been produced")

# Make nibabies input dirs
bibsnet_derivs_dir = os.path.join(j_args["optional_out_dirs"]["derivatives"],
"bibsnet")
derivs_dir = os.path.join(bibsnet_derivs_dir, *sub_ses, "anat")
os.makedirs(derivs_dir, exist_ok=True)
copy_to_derivatives_dir(nii_outfpath, derivs_dir, sub_ses, "aseg_dseg")
copy_to_derivatives_dir(aseg_mask, derivs_dir, sub_ses, "brain_mask")
for t in only_Ts_needed_for_bibsnet_model(j_args["ID"]):
nii_outfpath = reverse_regn_revert_to_native(
nifti_file_paths, chiral_out_dir, xfm_ref_img_dict[t], t, j_args, logger
)

logger.info("The BIBSnet segmentation has had its chirality checked and "
"registered if needed. Now making aseg-derived mask.")

# TODO Skip mask creation if outputs already exist and not j_args[common][overwrite]
aseg_mask = make_asegderived_mask(j_args, chiral_out_dir, t, nii_outfpath) # NOTE Mask must be in native T1 space too
logger.info(f"A mask of the BIBSnet T{t} segmentation has been produced")

# Make nibabies input dirs
bibsnet_derivs_dir = os.path.join(j_args["optional_out_dirs"]["derivatives"],
"bibsnet")
derivs_dir = os.path.join(bibsnet_derivs_dir, *sub_ses, "anat")
os.makedirs(derivs_dir, exist_ok=True)
copy_to_derivatives_dir(nii_outfpath, derivs_dir, sub_ses, t, "aseg_dseg")
copy_to_derivatives_dir(aseg_mask, derivs_dir, sub_ses, t, "brain_mask")

# Copy dataset_description.json into bibsnet_derivs_dir directory for use in nibabies
new_data_desc_json = os.path.join(bibsnet_derivs_dir, "dataset_description.json")
Expand Down Expand Up @@ -894,14 +890,15 @@ def run_left_right_registration(sub_ses, age_months, t1or2, j_args, logger):
return left_right_mask_nifti_fpath


def correct_chirality_revert_to_native(l_r_mask_nifti_fpath, j_args, logger):
def run_correct_chirality(l_r_mask_nifti_fpath, j_args, logger):
"""
:param l_r_mask_nifti_fpath: String, valid path to existing left/right
registration output mask file
:param j_args: Dictionary containing all args from parameter .JSON file
:param logger: logging.Logger object to show messages and raise warnings
:return: String, valid path to existing directory containing newly created
chirality correction outputs
:return nii_fpaths: Dictionary output of correct_chirality
:return chiral_out_dir: String file path to output directory
:return chiral_ref_img_fpaths_dict: Dictionary containing T1w and T2w file paths
"""
sub_ses = get_subj_ID_and_session(j_args)

Expand All @@ -924,11 +921,13 @@ def correct_chirality_revert_to_native(l_r_mask_nifti_fpath, j_args, logger):

# Select an arbitrary T1w image path to use to get T1w space
# (unless in T2w-only mode, in which case use an arbitrary T2w image)
t = 2 if not j_args["ID"]["has_T1w"] else 1
chiral_ref_img_fpaths = glob(os.path.join(
j_args["common"]["bids_dir"], *sub_ses, "anat", f"*_T{t}w.nii.gz"
))
chiral_ref_img_fpaths.sort()
chiral_ref_img_fpaths_dict = {}
for t in only_Ts_needed_for_bibsnet_model(j_args["ID"]):
chiral_ref_img_fpaths = glob(os.path.join(
j_args["common"]["bids_dir"], *sub_ses, "anat", f"*_T{t}w.nii.gz"
))
chiral_ref_img_fpaths.sort()
chiral_ref_img_fpaths_dict[t] = chiral_ref_img_fpaths[0]

# Run chirality correction script and return the image to native space
msg = "{} running chirality correction on " + seg_BIBSnet_outfiles[0]
Expand All @@ -937,25 +936,24 @@ def correct_chirality_revert_to_native(l_r_mask_nifti_fpath, j_args, logger):
seg_BIBSnet_outfiles[0], segment_lookup_table_path,
l_r_mask_nifti_fpath, chiral_out_dir
)
native_img_fpath = reverse_regn_revert_to_native(
nii_fpaths, chiral_out_dir, chiral_ref_img_fpaths[0], j_args, logger
)
logger.info(msg.format("Finished"))
return native_img_fpath

return nii_fpaths, chiral_out_dir, chiral_ref_img_fpaths_dict


def make_asegderived_mask(j_args, aseg_dir, nii_outfpath):
def make_asegderived_mask(j_args, aseg_dir, t, nii_outfpath):
"""
Create mask file(s) derived from aseg file(s) in aseg_dir
:param j_args: Dictionary containing all args from parameter .JSON file
:param aseg_dir: String, valid path to existing directory with output files
from chirality correction
:param t: 1 or 2, whether running on T1 or T2
:param nii_outfpath: String, valid path to existing anat file
:return: List of strings; each is a valid path to an aseg mask file
"""
# binarize, fillh, and erode aseg to make mask:
output_mask_fpath = os.path.join(
aseg_dir, "{}_mask.nii.gz".format(nii_outfpath.split(".nii.gz")[0])
aseg_dir, f"{nii_outfpath.split('.nii.gz')[0]}_T{t}_mask.nii.gz"
)
if (j_args["common"]["overwrite"] or not
os.path.exists(output_mask_fpath)):
Expand All @@ -967,16 +965,17 @@ def make_asegderived_mask(j_args, aseg_dir, nii_outfpath):
return output_mask_fpath


def copy_to_derivatives_dir(file_to_copy, derivs_dir, sub_ses, new_fname_pt):
def copy_to_derivatives_dir(file_to_copy, derivs_dir, sub_ses, space, new_fname_pt):
"""
Copy file_to_copy into derivs_dir and rename it with the other 2 arguments
:param file_to_copy: String, path to existing file to copy to derivs_dir
:param derivs_dir: String, path to existing directory to copy file into
:param sub_ses: List with either only the subject ID str or the session too
:param space: 1 or 2, the space which the mask/aseg is in
:param new_fname_pt: String to add to the end of the new filename
"""
shutil.copy2(file_to_copy, os.path.join(derivs_dir, (
"{}_space-orig_desc-{}.nii.gz".format("_".join(sub_ses), new_fname_pt)
"{}_space-T{}w_desc-{}.nii.gz".format("_".join(sub_ses), space, new_fname_pt)
)))


Expand Down
10 changes: 5 additions & 5 deletions src/utilities.py
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Original file line number Diff line number Diff line change
Expand Up @@ -370,7 +370,7 @@ def correct_chirality(nifti_input_file_path, segment_lookup_table,
:return: Dict with paths to native and chirality-corrected images
"""
nifti_file_paths = dict()
for which_nii in ("native", "corrected"):
for which_nii in ("native-T1", "native-T2", "corrected"):
nifti_file_paths[which_nii] = os.path.join(chiral_out_dir, "_".join((
which_nii, os.path.basename(nifti_input_file_path)
)))
Expand Down Expand Up @@ -1209,14 +1209,15 @@ def reshape_volume_to_array(array_img):


def reverse_regn_revert_to_native(nifti_file_paths, chiral_out_dir,
xfm_ref_img, j_args, logger):
xfm_ref_img, t, j_args, logger):
"""
:param nifti_file_paths: Dict with valid paths to native and
chirality-corrected images
:param chiral_out_dir: String, valid path to existing directory to save
chirality-corrected images into
:param xfm_ref_img: String, path to (T1w, unless running in T2w-only mode)
image to use as a reference when applying transform
:param t: 1 or 2, whether running on T1 or T2
:param j_args: Dictionary containing all args from parameter .JSON file
:param logger: logging.Logger object to show messages and raise warnings
:return: String, valid path to existing image reverted to native
Expand All @@ -1227,7 +1228,6 @@ def reverse_regn_revert_to_native(nifti_file_paths, chiral_out_dir,
# padding isn't necessary; revert aseg to native space
dummy_copy = "_dummy".join(split_2_exts(nifti_file_paths["corrected"]))
shutil.copy2(nifti_file_paths["corrected"], dummy_copy)
t = 2 if not j_args["ID"]["has_T1w"] else 1

seg2native = os.path.join(chiral_out_dir, f"seg_reg_to_T{t}w_native.mat")
preBIBSnet_mat_glob = os.path.join(
Expand All @@ -1241,9 +1241,9 @@ def reverse_regn_revert_to_native(nifti_file_paths, chiral_out_dir,

run_FSL_sh_script(j_args, logger, "flirt", "-applyxfm",
"-ref", xfm_ref_img, "-in", dummy_copy,
"-init", seg2native, "-o", nifti_file_paths["native"],
"-init", seg2native, "-o", nifti_file_paths[f"native-T{t}"],
"-interp", "nearestneighbour")
return nifti_file_paths["native"]
return nifti_file_paths[f"native-T{t}"]


def run_FSL_sh_script(j_args, logger, fsl_fn_name, *fsl_args):
Expand Down

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