def create_nifti_corrs_brain(corrs_atlas, sub, paths, SESSION_RESEARCH3T,
atlas_name):
ses = basename(
glob.glob(
join(paths.BIDS_DERIVATIVES_STRUCTURAL_MATRICES, f"sub-{sub}",
f"ses-{SESSION_RESEARCH3T}"))[0])[4:]
save_loc = join(paths.SEIZURE_SPREAD_ATLASES_PROBABILITIES, f"sub-{sub}")
utils.checkPathAndMake(save_loc, save_loc, printBOOL=False)
atlas_path = glob.glob(
join(paths.BIDS_DERIVATIVES_STRUCTURAL_MATRICES, f"sub-{sub}",
f"ses-{ses}", "atlas_registration", f"*{atlas_name}.nii.gz"))[0]
img, img_data = utils.load_img_and_data(atlas_path)
img_data_cors = copy.deepcopy(img_data)
img_data_cors[np.where(img_data_cors == 0)] = -1
#loop thru regions and replace regions with correlation data
for r in range(len(corrs_atlas)):
utils.printProgressBar(r + 1, len(corrs_atlas))
ind = np.where(img_data == int(corrs_atlas[r, 0]))
img_data_cors[ind] = float(corrs_atlas[r, 1])
save_loc_atlas = join(save_loc, f"{atlas_name}.nii.gz")
utils.save_nib_img_data(img_data_cors, img, save_loc_atlas)
T1_path = glob.glob(
join(paths.BIDS_DERIVATIVES_STRUCTURAL_MATRICES, f"sub-{sub}",
f"ses-{ses}", "atlas_registration",
"*desc-preproc_T1w_std.nii.gz"))[0]
if utils.checkIfFileDoesNotExist(f"{join(save_loc, basename(T1_path))}"):
utils.executeCommand(
cmd=f"cp {T1_path} {join(save_loc, basename(T1_path))}")
def freesurferReconAll(T1path, outputpath, overwrite=False, threads=12):
utils.checkPathErrorGlob(outputpath)
utils.checkPathErrorGlob(T1path)
if utils.checkIfFileDoesNotExist(f"{outputpath}/freesurfer/surf/lh.pial",
returnOpposite=overwrite):
if utils.checkIfFileDoesNotExist(
f"{outputpath}/freesurfer/surf/rh.pial",
returnOpposite=overwrite):
utils.executeCommand(f"mkdir -p {outputpath}/freesurfer/mri/orig")
utils.executeCommand(
f"mri_convert {T1path} {outputpath}/freesurfer/mri/orig/001.mgz"
)
utils.executeCommand(
f"recon-all -subjid freesurfer -all -time -log logfile -nuintensitycor-3T -sd {outputpath} -parallel -threads {threads}"
)
import os
from revellLab.packages.utilities import utils
import numpy as np
import glob
path1 = "/media/arevell/data/linux/data/BIDS/derivatives/structural_connectivity/structural_matrices"
path2 = "/home/arevell/Desktop/Berckerle_structure"
subs = np.sort(os.listdir(path1))
for i in range(len(subs)):
sub = subs[i]
print(
f"\r{sub} {i+1}/{len(subs)}, {np.round((i+1)/len(subs)*100,1)} ",
end="\r")
path_sub = os.path.join(path2, sub)
utils.checkPathAndMake(path_sub, path_sub, printBOOL=False)
sc_path = os.path.join(path1, sub, "ses-research3Tv[0-9][0-9]", "matrices",
"*connectogram.txt")
utils.checkPathErrorGlob(sc_path)
sc_paths_all = glob.glob(sc_path)
for sc in range(len(sc_paths_all)):
sc_p = sc_paths_all[sc]
cmd = f"cp {sc_p} {path_sub}"
utils.executeCommand(cmd, printBOOL=False)
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" ) ):
sessionPath = np.array(glob( join(freesurferReconAllDir, f"sub-{sub}", f"ses-{implantName}")))[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')} ")
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(
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} {T1wImagesCONTROLSDir}")
patients = pd.DataFrame(np.array(patients))
controls = pd.DataFrame(np.array(controls))
listOfFiles = list()
for (dirpath, dirnames, filenames) in os.walk(BIDSserver):
listOfFiles += [join(dirpath, file) for file in filenames]
for f in range(len(listOfFiles)):
#print(f)
SERVERfile = listOfFiles[f]
LOCALfile = join( BIDSlocal, relpath(SERVERfile, BIDSserver))
#ignore git
if not ".git" in relpath(SERVERfile, BIDSserver):
if utils.checkIfFileDoesNotExist(LOCALfile, printBOOL = False):
print(f"\n{LOCALfile}")
utils.checkPathAndMake( dirname(LOCALfile), dirname(LOCALfile), printBOOL = False )
utils.executeCommand( f"cp -r {SERVERfile} {LOCALfile}", printBOOL = False )
#%% Copy from local to server
listOfFiles = list()
for (dirpath, dirnames, filenames) in os.walk(BIDSlocal):
listOfFiles += [join(dirpath, file) for file in filenames]
for f in range(len(listOfFiles)):
print(f)
LOCALfile = listOfFiles[f]
SERVERfile = join( BIDSserver, relpath(LOCALfile, BIDSlocal))
#ignore git
if not ".git" in relpath(LOCALfile, BIDSlocal):