What do you see when you run ls -l $SUBJECTS_DIR/fsaverage/surf/lh.inflated
On 4/24/2020 11:55 AM, Sezer, Idil wrote:
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
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