search

psych-214-fall-2016 / project-red

Other
1 stars 7 forks source link

issues with file location? #66

Open jbpoline opened 7 years ago

jbpoline commented 7 years ago

When trying

python fmri_utils/func_preproc/volume_realignment.py -f sub-10159_task-restbold.nii -n 1 -s 5 -p r

as in the Makefile, in the code directory, I get :

FileNotFoundError: No such file: '/home/jb/code/psych214/project-red/data/sub-10159_task-rest_bold.nii'

ds000030 directory missing ?

see below for full trace :

Namespace(file='sub-10159_task-rest_bold.nii', numpass=1, prefix='r', smooth=5) Traceback (most recent call last): File "fmri_utils/func_preproc/volume_realignment.py", line 306, in main() File "fmri_utils/func_preproc/volume_realignment.py", line 302, in main run_realignment(args.file, smooth_fwhm = args.smooth, num_pass = args.num_pass, prefix = args.prefix) File "fmri_utils/func_preproc/volume_realignment.py", line 231, in run_realignment realigned_img, rp = volume_4D_realign(img_path, smooth_fwhm = smooth_fwhm, jitter = 0.1, prefix = prefix) File "fmri_utils/func_preproc/volume_realignment.py", line 69, in volume_4D_realign img = nib.load(img_path) File "/home/jb/virtualenvs/red/lib/python3.5/site-packages/nibabel/loadsave.py", line 40, in load raise FileNotFoundError("No such file: '%s'" % filename) FileNotFoundError: No such file: '/home/jb/code/psych214/project-red/data/sub-10159_task-rest_bold.nii'