Hello
FreeSurfer developers,
I
am having an issue viewing a .mgh file I created.
Using
an output from the fmriprep pipeline, I converted an nii.gz
to a .mgh surface :
mri_vol2surf --src
<participant_ID>_desc-preproc_T1w.nii.gz
--<participant_ID> --regheader <participant_ID>
--hemi lh
I
am trying to visualize this surface on an inflated brain
using:
freeview
-f
$SUBJECTS_DIR/fsaverage/surf/lh.inflated:overlay=/Users/idilsezer/Desktop/fmriprep_outputs/test/lh.<participant_ID>.mgh
I get an error message saying :
MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated):
could not open file
No
such file or directory
MRISread
failed
MRISread(/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated):
could not open file
And Freeview’s GUI says : Failed
to load Surface
/Users/idilsezer/Desktop/fmriprep_outputs/freesurfer/fsaverage/surf/lh.inflated
I also tried
loading it directly from the GUI instead of the command
line, it also doesn’t seem to work unfortunately.
FreeSurfer
version : freesurfer-Darwin-OSX-stable-pub-v6.0.0-2beb96c
Platform : mac OS
Catalina version 10.15.4 (19E287)
Thanks in advance
for your help,
Best regards,
Idil