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 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 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}"
)
def make_spherical_regions(patient_list, SESSION, paths, radius = 7, rerun = False, show_slices = False):
N = len(patient_list)
for i in range(N):
sub = patient_list[i]
print(sub)
localization, localization_channels = atl.get_atlas_localization_file(sub, SESSION, paths)
#t1_image = join(paths['BIDS'], "PIER", f"sub-{sub}", f"ses-{ses}", "anat", f"sub-{sub}_ses-{ses}_space-T1w_desc-preproc_dwi.nii.gz" )
t1_image = glob.glob(join(paths.BIDS_DERIVATIVES_ATLAS_LOCALIZATION, f"sub-{sub}", f"ses-{SESSION}", "tmp", "orig_nu_std.nii.gz" ))[0]
img = nib.load(t1_image)
if show_slices: utils.show_slices(img, data_type = "img")
img_data = img.get_fdata()
affine = img.affine
shape = img_data.shape
coordinates = np.array(localization[["x", "y", "z"]])
coordinates_voxels = utils.transform_coordinates_to_voxel(coordinates, affine)
path_spheres = join(paths.BIDS_DERIVATIVES_TRACTOGRAPHY, f"sub-{sub}", "electrodeContactSphereROIs")
utils.checkPathAndMake(path_spheres, path_spheres, printBOOL = False)
for e in range(len(localization_channels)):
fname_ROIs_sub_ID = join(path_spheres, f"sub-{sub}_ses-implant01_desc-{localization_channels[e]}.nii.gz")
if utils.checkIfFileDoesNotExist(fname_ROIs_sub_ID, printBOOL = False) or rerun:
img_data_sphere = copy.deepcopy(img_data)
img_data_sphere[ np.where(img_data_sphere != 0) ] = 0
x = coordinates_voxels[e][0]
y = coordinates_voxels[e][1]
z = coordinates_voxels[e][2]
img_data_sphere = utils.make_sphere_from_point(img_data_sphere, x, y, z, radius = radius) #radius = 7mm
img_sphere = nib.Nifti1Image(img_data_sphere, img.affine)
nib.save(img_sphere, fname_ROIs_sub_ID)
#utils.show_slices(img_data_sphere, data_type = "data")
utils.printProgressBar(e+1, len(localization_channels))
with open(analysis_location_file, 'rb') as f:
[
X, y, fsds, secondsBefore, secondsAfter, window,
skipWindow, montage
] = pickle.load(f)
X_train = np.concatenate([X_train, X], axis=0)
y_train = np.concatenate([y_train, y], axis=0)
# LL
version = 100 + k
feature_name = "line_length"
filepath = join(deepLearningModelsPath,
f"single_features/{feature_name}_v{version:03d}.hdf5")
if utils.checkIfFileDoesNotExist(filepath, printBOOL=False):
lineLength_arr_train, lineLengthNorm_train = echobase.line_length_x_train(
X_train)
lineLength_arr_test, lineLengthNorm_test = echobase.line_length_x_train(
X_test)
lineLength_arr_test_norm = lineLength_arr_test / np.max(
lineLength_arr_train)
analysis = [
lineLength_arr_train, lineLengthNorm_train, lineLength_arr_test,
lineLengthNorm_test, lineLength_arr_test_norm
]
with open(filepath, 'wb') as f:
pickle.dump(analysis, f)
else:
#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')} ")
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'surf' , 'rh.pial')} {join(outputpath, 'freesurfer', 'surf')} ")
else:
continue
#check if lh and rh.pial have been moved to implantRenders derivatives path properly
if utils.checkIfFileDoesNotExist(f"{outputpath}/html/brain.glb", returnOpposite=False):
if utils.checkIfFileExists(f"{join(outputpath, 'freesurfer', 'surf' ,'lh.pial')}" ) and utils.checkIfFileExists( f"{join(outputpath, 'freesurfer', 'surf' ,'rh.pial')}") :
# combined surfs
utils.executeCommand( f"cp {outputpath}/freesurfer/surf/lh.pial {outputpath}/freesurfer/" )
utils.executeCommand( f"cp {outputpath}/freesurfer/surf/rh.pial {outputpath}/freesurfer/" )
utils.executeCommand( f"mris_convert --to-scanner {outputpath}/freesurfer/lh.pial {outputpath}/freesurfer/lh.pial" )
utils.executeCommand( f"mris_convert --to-scanner {outputpath}/freesurfer/rh.pial {outputpath}/freesurfer/rh.pial" )
utils.executeCommand( f"mris_convert --combinesurfs {outputpath}/freesurfer/rh.pial {outputpath}/freesurfer/lh.pial {outputpath}/freesurfer/combined.stl" )
cmd = f"blender --background --factory-startup --addons io_scene_gltf2 --python {revellLabPath}/packages/imaging/electrodeLocalization/blender_compress_mesh.py -- -i {outputpath}/freesurfer/combined.stl -o {outputpath}/html/brain.glb"
utils.executeCommand(cmd)
utils.executeCommand(f"cp {join(sessionPath, 'freesurfer', 'mri' , 'aseg.mgz')} {join(outputpath, 'freesurfer', 'mri' )} ")
outputDirTMP = join(outputpath, "freesurfer")
T1 =join(outputpath, 'freesurfer', 'mri', 'orig_nu.mgz' )
T1brain =join(outputpath, 'freesurfer', 'mri', 'brain.mgz' )
aseg =join(outputpath, 'freesurfer', 'mri', 'aseg.mgz' )
T00 = glob(T00)[0]
#%% Copy from server to local
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]