Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz
what does it show?
On Aug 9, 2017, at 4:47 PM, Z Hessam z.hessam@gmail.com wrote:
of course:
hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v bert/mri/T1.mgz bert/mri/wm.mgz bert/mri/brainmask.mgz bert/mri/aseg.mgz:colormap=lut:opacity=0.2 -f bert/surf/lh.white:edgecolor=blue bert/surf/lh.pial:edgecolor=red bert/surf/rh.white:edgecolor=blue bert/surf/rh.pial:edgecolor=red
mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz mghRead(/media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz, -1): read error
thanks a lot for your attention
On Wed, Aug 9, 2017 at 10:57 PM, Ruopeng Wang <rpwang@nmr.mgh.harvard.edu mailto:rpwang@nmr.mgh.harvard.edu> wrote: Can you copy and paste the exact command line you ran and the error message?
Ruopeng
On 08/09/2017 02:21 PM, Z Hessam wrote:
I try it without \ chars, works for some other subjects but it doesn't work for one of them,and now I can even open it with GUI, while I could open it before. It seems that is time variant! Should I run "recon-all ..." again for that subject?
On Wed, Aug 9, 2017 at 10:32 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote: can you try it without all the \ characters? You shouldn't need them if it's all on one line
On Wed, 9 Aug 2017, Z Hessam wrote:
$>freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/ MRIread failed: Unable to read from /media/hessam91/driver2/freesurfer/freesurfer/subjects/ mri_read(): couldn't determine type of file /media/hessam91/driver2/freesurfer/freesurfer/subjects/
I use the example 4 in the "download and install" page of site
On Wed, Aug 9, 2017 at 8:44 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
hmmm, that looks ok, but it's hard to tell with all the backslashes and blank lines and such. Can you send the full command on a single line (e.g. by hitting up-arrow in the terminal window) and the actual output of freeview? On Wed, 9 Aug 2017, Z Hessam wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", mri_read(): couldn't determine type of file <subject_dir> MRIread failed: Unable to read from <subject_dir> mri_read(): couldn't determine type of file <subject_dir> but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards On Wed, Aug 9, 2017 at 7:56 PM, Z Hessam <z.hessam@gmail.com <mailto:z.hessam@gmail.com>> wrote: Hello Freesurfer Developers, I have problem when I use "freeview" example code in terminal, freeview -v \ bert/mri/T1.mgz \ bert/mri/wm.mgz \ bert/mri/brainmask.mgz \ bert/mri/aseg.mgz:colormap=lut:opacity=0.2 \ -f \ bert/surf/lh.white:edgecolor=blue \ bert/surf/lh.pial:edgecolor=red \ bert/surf/rh.white:edgecolor=blue \ bert/surf/rh.pial:edgecolor=red it tell "Failed to load MRI <subject_dir>", but i can load wm.mgz and other existed files in GUI. please help me to know why this error happend? and what should I do to solve this? I've searched the list, I found a similar errors, but wasn't helpful answer reported. help me please regards
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