def get_tracts_loop_through_patient_list(
patient_list,
paths,
singularity_bind_path=None,
path_dsiStudioSingularity=None,
SESSION_RESEARCH3T="research3Tv[0-9][0-9]"):
if singularity_bind_path == None:
singularity_bind_path = paths.BIDS
if path_dsiStudioSingularity == None:
path_dsiStudioSingularity = paths.DSI_STUDIO_SINGULARITY
N = len(patient_list)
for i in range(N):
sub = patient_list[i]
ses = basename(
glob.glob(
join(paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}"))[0])[4:]
path_dwi = join(
paths.BIDS_DERIVATIVES_QSIPREP, "qsiprep", f"sub-{sub}",
f"ses-{ses}", "dwi",
f"sub-{sub}_ses-{ses}_space-T1w_desc-preproc_dwi.nii.gz")
path_tracts = join(paths.BIDS_DERIVATIVES_TRACTOGRAPHY, f"sub-{sub}",
f"ses-{ses}")
utils.checkPathAndMake(path_tracts, path_tracts, printBOOL=False)
utils.checkIfFileExistsGlob(path_dwi, printBOOL=False)
trk_name = f"{join(path_tracts, utils.baseSplitextNiiGz(path_dwi)[2])}.trk.gz"
if utils.checkIfFileDoesNotExist(trk_name):
get_tracts(singularity_bind_path, path_dsiStudioSingularity,
path_dwi, path_tracts)
def get_patients_with_dwi(subject_list,
paths,
dataset="PIER",
SESSION_RESEARCH3T="research3Tv[0-9][0-9]"):
sfc_patient_list = []
N = len(subject_list)
for i in range(N):
sub = subject_list[i]
dwi_path = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "dwi", "*_dwi.nii.gz")
dwi_path_json = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "dwi", "*_dwi.json")
dwi_path_bvec = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "dwi", "*_dwi.bvec")
dwi_path_bval = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "dwi", "*_dwi.bval")
dwi_path_fmap_phasediff = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "fmap",
"*_phasediff.nii.gz")
dwi_path_fmap_topup = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "fmap",
"*_epi.nii.gz")
dwi_path_fmap_T1 = join(paths.BIDS, "PIER", f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}", "anat",
f"*acq-3D_T1w.nii.gz")
exists = all([
utils.checkIfFileExistsGlob(dwi_path, printBOOL=False),
utils.checkIfFileExistsGlob(dwi_path_json, printBOOL=False),
utils.checkIfFileExistsGlob(dwi_path_bvec, printBOOL=False),
utils.checkIfFileExistsGlob(dwi_path_bval, printBOOL=False),
utils.checkIfFileExistsGlob(dwi_path_fmap_T1, printBOOL=False)
])
#check if all the necessary imaging files for correction exists
if exists:
#check if phasediff or topup exists
if any([
utils.checkIfFileExistsGlob(dwi_path_fmap_phasediff,
printBOOL=False),
utils.checkIfFileExistsGlob(dwi_path_fmap_topup,
printBOOL=False)
]):
sfc_patient_list.append(sub)
sfc_patient_list = list(np.unique(sfc_patient_list))
return sfc_patient_list
for imp in range(len(implantList)):
implantName = implantList[imp]
preferredSurface = "research3T*"
for s in range(0,len(subjects)):
#sub = "RID0030"
sub = subjects[s][4:]
print(sub)
derivativesOutput = "implantRenders"
T00 = join(BIDS, dataset, f"sub-{sub}", f"ses-{implantName}", "anat", f"sub-{sub}_ses-{implantName}_acq-T00_*T1w.nii.gz" )
T00electrodes = join(BIDS, dataset, f"sub-{sub}", f"ses-{implantName}", "ieeg", f"sub-{sub}_ses-{implantName}_space-T00_electrodes.tsv" )
if utils.checkIfFileExistsGlob(T00) and utils.checkIfFileExistsGlob(T00electrodes):
#check if freesurfer has been run on preferred session
if utils.checkIfFileExistsGlob( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{preferredSurface}", "freesurfer", "surf", "lh.pial" ) ) and utils.checkIfFileExistsGlob( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{preferredSurface}", "freesurfer", "surf", "rh.pial" ) ):
sessionPath = np.array(glob( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{preferredSurface}")))[0]
session = basename(sessionPath)[4:]
outputpath = join(BIDS, "derivatives", f"{derivativesOutput}", f"sub-{sub}", f"ses-{session}")
utils.checkPathAndMake(outputpath, join(outputpath, "freesurfer", 'mri' ))
utils.checkPathAndMake(outputpath, join(outputpath, "freesurfer", 'surf' ))
utils.checkPathAndMake(outputpath, join(outputpath, "html"))
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'mri' , 'orig_nu.mgz')} {join(outputpath, 'freesurfer', 'mri' )} ")
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'mri' , 'brain.mgz')} {join(outputpath, 'freesurfer', 'mri' )} ")
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'surf' , 'lh.pial')} {join(outputpath, 'freesurfer', 'surf')} ")
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'surf' , 'rh.pial')} {join(outputpath, 'freesurfer', 'surf')} ")
#check if freesurfer has been run on implant session
elif utils.checkIfFileExists( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{implantName}", "freesurfer", "surf", "lh.pial" ) ) and utils.checkIfFileExists( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{implantName}", "freesurfer", "surf", "rh.pial" ) ):
utils.checkPathAndMake(outputDir, T1wDirTemplatePatients02)
acq = "3D"
ses = "research3T*"
#going thru BIDS directory to get paths of controls and patients
patients = []
controls = []
for s in range(len(subDir)):
#sub = "RID0588"
subjectPath = subDir[s]
sub = basename(subjectPath)[4:]
print(sub)
if utils.checkIfFileExistsGlob(
join(subjectPath, f"ses-{ses}", "anat",
f"sub-{sub}_ses-{ses}_acq-{acq}_T1w.nii.gz")):
if sub not in ControlsList:
patients.append(
glob(
join(subjectPath, f"ses-{ses}", "anat",
f"sub-{sub}_ses-{ses}_acq-{acq}_T1w.nii.gz")))
file = glob(
join(subjectPath, f"ses-{ses}", "anat",
f"sub-{sub}_ses-{ses}_acq-{acq}_T1w.nii.gz"))[0]
if utils.checkIfFileDoesNotExistGlob(f"{file}"):
utils.executeCommand(f"cp {file} {T1wImagesPATEINTSDir}")
if sub in ControlsList:
controls.append(
glob(
LINUX_BIDSserver = join("/home/arevell/borel/DATA/Human_Data/BIDS", "PIER")
#
#updating intended for in fmap json files:
directories = os.listdir(LINUX_BIDSserver)
ses_research3T = "research3Tv[0-9][0-9]"
for i in range(len(directories)):
file = directories[i]
if "sub-RID" in file:
sub = file
if utils.checkIfFileExistsGlob(join(LINUX_BIDSserver, sub,
f"ses-{ses_research3T}"),
printBOOL=False):
ses_folder = glob.glob(
join(LINUX_BIDSserver, sub, f"ses-{ses_research3T}"))[0]
ses = basename(ses_folder)[4:]
if utils.checkIfFileExistsGlob(join(LINUX_BIDSserver, sub,
f"ses-{ses}", "func",
"*rest_bold.nii.gz"),
printBOOL=False): #if fMRI exists
fMRI_path = glob.glob(
join(LINUX_BIDSserver, sub, f"ses-{ses}", "func",
"*rest_bold.nii.gz"))[0]
fMRI_path_basename = basename(fMRI_path)
fMRI_IntendedFor = join(f"ses-{ses}", "func",