def getBIDSinputAndOutput(BIDS, dataset, sub, ses, acq, derivativesOutput):
T1path = join(BIDS, dataset, f"sub-{sub}", f"ses-{ses}", "anat",
f"sub-{sub}_ses-{ses}_acq-{acq}_T1w.nii.gz")
utils.checkPathError(T1path)
out = join(BIDS, "derivatives", f"{derivativesOutput}")
utils.checkPathError(out)
outputpath = join(BIDS, "derivatives", f"{derivativesOutput}",
f"sub-{sub}", f"ses-{ses}")
utils.checkPathAndMake(outputpath, outputpath)
return T1path, outputpath
def applywarp_to_atlas(atlas_directory, atlas_paths, preop_T1_std, mni_warp,
atlas_registration_output_path):
full_atlas_paths = []
for a in range(len(atlas_paths)):
utils.checkPathError(
f"{os.path.join(atlas_directory, atlas_paths[a])}")
full_atlas_paths.append(
f"{os.path.join(atlas_directory, atlas_paths[a])}")
utils.checkPathError(mni_warp)
utils.checkPathError(preop_T1_std)
utils.checkPathError(atlas_registration_output_path)
for a in range(len(full_atlas_paths)):
atlasName = basename(splitext(splitext(full_atlas_paths[a])[0])[0])
outputAtlasName = join(atlas_registration_output_path,
atlasName + ".nii.gz")
#if not os.path.exists(outputAtlasName):
print(
f"\r{np.round((a+1)/len(full_atlas_paths)*100,2)}% {atlasName[0:20]} ",
end="\r")
if not utils.checkIfFileExists(outputAtlasName, printBOOL=False):
cmd = f"applywarp -i { full_atlas_paths[a]} -r {preop_T1_std} -w {mni_warp} --interp=nn -o {outputAtlasName}"
os.system(cmd)
def get_tracts(singularity_bind_path, path_dsiStudioSingularity, path_dwi,
output_directory):
utils.checkPathError(singularity_bind_path)
utils.checkPathError(path_dsiStudioSingularity)
utils.checkPathError(path_dwi)
utils.checkPathError(output_directory)
base, split, basesplit = utils.baseSplitextNiiGz(path_dwi)
source_name = f"{join(output_directory, basesplit)}.src.gz"
fib_name = f"{join(output_directory, basesplit)}.fib.gz"
trk_name = f"{join(output_directory, basesplit)}.trk.gz"
print("\n\nCreating Source File in DSI Studio\n\n")
cmd = f"singularity exec --bind {singularity_bind_path} {path_dsiStudioSingularity} dsi_studio --action=src --source={path_dwi} --output={source_name}"
os.system(cmd)
print("\n\nCreating Reconstruction File in DSI Studio\n\n")
cmd = f"singularity exec --bind {singularity_bind_path} {path_dsiStudioSingularity} dsi_studio --action=rec --source={source_name} --method=4 --param0=1.25"
os.system(cmd)
#rename dsistudio output of .fib file because there is no way to output a specific name on cammnad line
cmd = f"mv {source_name}*.fib.gz {fib_name}"
os.system(cmd)
print("\n\nCreating Tractography File in DSI Studio\n\n")
cmd = f"singularity exec --bind {singularity_bind_path} {path_dsiStudioSingularity} dsi_studio --action=trk --source={fib_name} --min_length=10 --max_length=800 --thread_count=16 --fiber_count=1000000 --output={trk_name}"
os.system(cmd)
f"sub-{sub}", f"ses-{ses}", "matrices")
utils.checkPathAndMake(atlas_registration, atlas_registration, printBOOL=False)
utils.checkPathAndMake(structural_matrices,
structural_matrices,
printBOOL=False)
preop_T1 = os.path.join(paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep",
f"sub-{sub}", "anat",
f"sub-{sub}_desc-preproc_T1w.nii.gz")
preop_T1_mask = os.path.join(paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep",
f"sub-{sub}", "anat",
f"sub-{sub}_desc-brain_mask.nii.gz")
preop_T1_bet = os.path.join(atlas_registration,
f"sub-{sub}_desc-preproc_T1w_brain.nii.gz")
utils.checkPathError(preop_T1)
utils.checkPathError(preop_T1_mask)
utils.checkPathError(paths.MNI_TEMPLATE)
utils.checkPathError(paths.MNI_TEMPLATE_BRAIN)
utils.checkPathError(paths.ATLASES)
utils.checkPathError(paths.ATLAS_FILES_PATH)
utils.checkPathError(structural_matrices)
cmd = f"cp {preop_T1} {os.path.join(atlas_registration, os.path.basename(preop_T1))}"
os.system(cmd)
cmd = f"cp {preop_T1_mask} {os.path.join(atlas_registration, os.path.basename(preop_T1_mask))}"
os.system(cmd)
cmd = f"fslmaths {preop_T1} -mul {preop_T1_mask} {preop_T1_bet}"
os.system(cmd)
preop_T1 = os.path.join(atlas_registration, os.path.basename(preop_T1))
raise IOError(
f"\n\n\n\nOutput Name must end with .csv.\n\nWhat is given:\n{outputName}\n\n\n\n"
)
print(
f"\n\n\n\n\n\n\n\n\n\n{outputName} saving to: \n{join(outputDirectory, outputName)}\n\n\n\n"
)
fillerString = "\n###########################\n###########################\n###########################\n###########################\n"
#atl.get_electrodeTissueMetadata(join(outputDirectory, outputName), join(outputDirectory, "electrodeTissueMetadata.json"))
if os.path.exists(join(outputDirectory, outputName)):
print(
f"\n\nNote: Electrode localization file alread exists in \n{join(outputDirectory, outputName)}\n"
)
if rerun == False:
sys.exit()
"""
Examples:
#electrodePreopT1Coordinates = "/media/arevell/sharedSSD/linux/data/BIDS/PIER/sub-RID0648/ses-implant01/ieeg/sub-RID0648_ses-implant01_space-preimplantT1w_electrodes.tsv"
electrodePreopT1Coordinates = "/media/arevell/sharedSSD/linux/data/BIDS/derivatives/atlasLocalization/sub-RID0648/electrodenames_coordinates_native_and_T1.csv"
preopT1 = "/media/arevell/sharedSSD/linux/data/BIDS/derivatives/atlasLocalization/sub-RID0648/T00_RID0648_mprage.nii.gz"
preopT1bet = "/media/arevell/sharedSSD/linux/data/BIDS/derivatives/atlasLocalization/sub-RID0648/T00_RID0648_mprage_brainBrainExtractionBrain.nii.gz"
MNItemplate = "/media/arevell/sharedSSD/linux/revellLab/tools/mniTemplate/mni_icbm152_t1_tal_nlin_asym_09c_182x218x182.nii.gz"
MNItemplatebet = "/media/arevell/sharedSSD/linux/revellLab/tools/mniTemplate/mni_icbm152_t1_tal_nlin_asym_09c_182x218x182_brain.nii.gz"
atlasDirectory = "/media/arevell/sharedSSD/linux/revellLab/tools/atlases/atlases"
atlasLabelsPath = "/media/arevell/sharedSSD/linux/revellLab/tools/atlases/atlasLabels"
outputDirectory = "/media/arevell/sharedSSD/linux/data/BIDS/derivatives/atlasLocalization/sub-RID0648"
outputName = "sub-RID0648_atlasLocalization.csv"
utils.checkPathError(electrodePreopT1Coordinates)
def mni_registration_to_T1(sub,
paths,
SESSION_RESEARCH3T="research3Tv[0-9][0-9]"):
#getting directories and files
#structural connectivity derivatives
atlas_registration, structural_matrices, mni_images, mni_warp, ses, preop_T1, preop_T1_std, path_fib, path_trk = get_atlas_registration_and_tractography_paths(
sub=sub, paths=paths, SESSION_RESEARCH3T=SESSION_RESEARCH3T)
if not utils.checkIfFileExists(f"{mni_images}_fnirt.nii.gz",
printBOOL=False):
#QSI prep outputs
preop_T1 = os.path.join(paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep",
f"sub-{sub}", "anat",
f"sub-{sub}_desc-preproc_T1w.nii.gz")
preop_T1_mask = os.path.join(paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep",
f"sub-{sub}", "anat",
f"sub-{sub}_desc-brain_mask.nii.gz")
preop_T1_bet = os.path.join(
atlas_registration, f"sub-{sub}_desc-preproc_T1w_brain.nii.gz")
#checking all images exist
utils.checkPathError(preop_T1)
utils.checkPathError(preop_T1_mask)
utils.checkPathError(paths.MNI_TEMPLATE)
utils.checkPathError(paths.MNI_TEMPLATE_BRAIN)
#copying relevant images from QSI prep to registration folder
cmd = f"cp {preop_T1} {os.path.join(atlas_registration, os.path.basename(preop_T1))}"
os.system(cmd)
cmd = f"cp {preop_T1_mask} {os.path.join(atlas_registration, os.path.basename(preop_T1_mask))}"
os.system(cmd)
cmd = f"fslmaths {preop_T1} -mul {preop_T1_mask} {preop_T1_bet}"
os.system(cmd)
#intemediary files output names
preop_T1 = os.path.join(atlas_registration, os.path.basename(preop_T1))
preop_T1_mask = os.path.join(atlas_registration,
os.path.basename(preop_T1_mask))
preop_T1_std = f"{splitext(splitext(preop_T1)[0])[0]}_std.nii.gz"
preop_T1_bet_std = f"{splitext(splitext(preop_T1_bet)[0])[0]}_std.nii.gz"
#Begin Pipeline: Orient all images to standard RAS
fillerString = "\n###########################" * 3
print(
f"\n\n{fillerString}\nPart 1 of 2\nReorientation of Images\nEstimated time: 10-30 seconds{fillerString}\nReorient all images to standard RAS\n"
)
cmd = f"fslreorient2std {preop_T1} {preop_T1_std}"
print(cmd)
os.system(cmd)
cmd = f"fslreorient2std {preop_T1_bet} {preop_T1_bet_std}"
print(cmd)
os.system(cmd)
#visualize
utils.show_slices(f"{preop_T1_std}",
low=0.33,
middle=0.5,
high=0.66,
save=True,
saveFilename=join(atlas_registration, "pic_T1.png"))
utils.show_slices(f"{preop_T1_bet_std}",
low=0.33,
middle=0.5,
high=0.66,
save=True,
saveFilename=join(atlas_registration,
"pic_T1_brain.png"))
#Registration of MNI to patient space (atlases are all in MNI space, so using this warp to apply to the atlases)
print(
f"\n\n{fillerString}\nPart 2 of 2\nMNI and atlas registration\nEstimated time: 1-2+ hours{fillerString}\nRegistration of MNI template to patient space\n"
)
#linear reg of MNI to preopT1 space
if not utils.checkIfFileExists(f"{mni_images}_flirt.nii.gz",
printBOOL=False):
cmd = f"flirt -in {paths.MNI_TEMPLATE_BRAIN} -ref {preop_T1_bet_std} -dof 12 -out {mni_images}_flirt -omat {mni_images}_flirt.mat -v"
print(cmd)
os.system(cmd)
#non linear reg of MNI to preopT1 space
utils.show_slices(f"{mni_images}_flirt.nii.gz",
low=0.33,
middle=0.5,
high=0.66,
save=True,
saveFilename=join(atlas_registration,
"pic_mni_to_T1_flirt.png"))
print(
"\n\nLinear registration of MNI template to image is done\n\nStarting Non-linear registration:\n\n\n"
)
if not utils.checkIfFileExists(f"{mni_images}_fnirt.nii.gz",
printBOOL=False):
cmd = f"fnirt --in={paths.MNI_TEMPLATE} --ref={preop_T1_std} --aff={mni_images}_flirt.mat --iout={mni_images}_fnirt -v --cout={mni_images}_coef --fout={mni_images}_warp"
print(cmd)
os.system(cmd)
utils.show_slices(f"{mni_images}_fnirt.nii.gz",
low=0.33,
middle=0.5,
high=0.66,
save=True,
saveFilename=join(atlas_registration,
"pic_mni_to_T1_fnirt.png"))
print(f"\n\n{fillerString}\nDone{fillerString}\n\n\n\n")
else:
print(f"\n\n\n\nMNI registration already performed\n\n\n\n")
def get_structural_connectivity(singularity_bind_path,
path_dsiStudioSingularity, path_fib, path_trk,
preop3T, atlas, output):
utils.checkPathError(singularity_bind_path)
utils.checkPathError(path_dsiStudioSingularity)
utils.checkPathError(path_fib)
utils.checkPathError(path_trk)
utils.checkPathError(preop3T)
utils.checkPathError(atlas)
cmd = f"singularity exec --bind {singularity_bind_path} {path_dsiStudioSingularity} dsi_studio --action=ana --source={path_fib} --tract={path_trk} --t1t2={preop3T} --connectivity={atlas} --connectivity_type=pass --connectivity_threshold=0 --output={output}"
os.system(cmd)