if not os.path.exists(outpathbval) or not os.path.exists(outpathbvec) or overwrite:
mkcdir(outpathsubj)
writeformat="tab"
writeformat="dsi"
bvals = glob.glob(os.path.join(outpath, "*bvals*.txt"))
bvecs = glob.glob(os.path.join(outpath, "*bvec*.txt"))
if np.size(bvals)>0 and np.size(bvecs)>0:
shutil.copy(bvals[0], outpathbval)
shutil.copy(bvecs[0], outpathbvec)
results=[]
if subject_processes>1:
if function_processes>1:
pool = MyPool(subject_processes)
else:
pool = mp.Pool(subject_processes)
results = pool.starmap_async(launch_preprocessing, [(proc_subjn+subject,
largerfile(glob.glob(os.path.join(os.path.join(diffpath, "*" + subject + "*")))[0]),
outpath, cleanup, nominal_bval, bonusshortcutfolder,
gunniespath, function_processes, masking, ref, transpose,
overwrite, denoise, recenter, verbose)
for subject in subjects]).get()
else:
for subject in subjects:
max_size=0
subjectpath = glob.glob(os.path.join(os.path.join(diffpath, "*" + subject + "*")))[0]
max_file=largerfile(subjectpath)
launch_preprocessing(proc_subjn+subject, max_file, outpath, cleanup, nominal_bval, bonusshortcutfolder,
gunniespath, function_processes, masking, ref, transpose, overwrite, denoise, recenter, verbose)
else:
for subject in subjects:
max_size = 0
subjectpath = glob.glob(
os.path.join(os.path.join(outpath,
"diffusion*" + subject + "*")))[0]
print(subjectpath)
max_file = largerfile(subjectpath)
max_file = os.path.join(subjectpath,
"nii4D_" + proc_subjn + subject + ".nii.gz")
print(max_file)
#command = gunniespath + "mouse_diffusion_preprocessing.bash"+ f" {subject} {max_file} {outpath}"
subject_f = proc_subjn + subject
if os.path.exists(
os.path.join(
'/mnt/munin6/Badea/Lab/mouse/ADDeccode_symlink_pool/',
f'{subject_f}_subjspace_coreg.nii.gz')):
print(
f'Could not find subject {subject_f} in main diffusion folder but result was found in SAMBA prep folder'
)
#elif os.path.exists(os.path.join('/mnt/munin6/Badea/Lab/mouse/VBM_21ADDecode03_IITmean_RPI_fullrun-work/dwi/SyN_0p5_3_0p5_fa/faMDT_NoNameYet_n37_i6/reg_images/',f'{subject_f}_rd_to_MDT.nii.gz')):
# print(f'Could not find subject {subject_f} in main diff folder OR samba init but was in results of SAMBA')
else:
launch_preprocessing(proc_subjn + subject, max_file, outpath,
cleanup, nominal_bval, SAMBA_inputs_folder,
shortcuts_all_folder, gunniespath,
function_processes, masking, ref, transpose,
overwrite, denoise, verbose)
#results.append(launch_preprocessing(subject, max_file, outpath))
results = pool.starmap_async(launch_preprocessing, [
(subject,
largerfile(
glob.glob(os.path.join(os.path.join(
dwipath, "*" + subject + "*")))[0]), outpath)
for subject in subjects
]).get()
else:
for subject in subjects:
max_size = 0
subjectpath = glob.glob(
os.path.join(os.path.join(dwipath, "*" + subject + "*")))[0]
max_file = largerfile(subjectpath)
#command = gunniespath + "mouse_diffusion_preprocessing.bash"+ f" {subject} {max_file} {outpath}"
launch_preprocessing(subject,
max_file,
outpath,
nominal_bval=800,
shortcutpath=shortcutpath,
bonusniftipath=None,
gunniespath="/Users/alex/bass/gitfolder/gunnies/",
matlabpath="/Users/alex/Documents/MATLAB/")
#results.append(launch_preprocessing(subject, max_file, outpath))
"""
subjectlist = ["58215","58216","58217","58218","58219","58221","58222","58223","58224","58225","58226","58228","58229","58230","58231","58232","58633","58634","58635","58636","58649","58650","58651","58653","58654"]
for subj in subjectlist:
fbvals_new = fbvals.replace("58214", subj)
shutil.copyfile(fbvals, fbvals_new)
fbvecs_new = fbvals.replace("58214", subj)
shutil.copyfile(fbvals, fbvals_new)
"""