Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Sure. Please make sure you have as much as spare disk space as you can. > On Aug 10, 2017, at 4:12 PM, Z Hessam wrote: > > it seems that I should run it again > thank you for your helps > best regards > > On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

it seems that I should run it again thank you for your helps best regards On Thu, Aug 10, 2017 at 6:27 PM, Ruopeng Wang wrote: > OK. Actually I was wrong, the file has size of 0! I don’t know what > happened when you installed freesurfer or ran recon-all, but the

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

OK. Actually I was wrong, the file has size of 0! I don’t know what happened when you installed freesurfer or ran recon-all, but the file was not properly written... > On Aug 10, 2017, at 9:34 AM, Z Hessam wrote: > > I copy the *.tar.gz file, and open and install the

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

I copy the *.tar.gz file, and open and install the program by terminal. I am confused because that work last week for this data, but now, this doesn't work. for other datasets, i copy dicom files, then convert them with " recon-all -i STRUCT_FOLDER1/xxx.dcm -i STRUCT_FOLDER2/xxx.dcm -autorecon1

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

How did you put the data on your drive? > On Aug 10, 2017, at 9:25 AM, Z Hessam wrote: > > I didn't copy the file, and drive has 3.7GB free space > > On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang > wrote: >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

I didn't copy the file, and drive has 3.7GB free space On Thu, Aug 10, 2017 at 5:41 PM, Ruopeng Wang wrote: > Wait, the file size looks too small. Only 1590 bytes. Did the data get > copied properly? Is your drive full? > > On Aug 10, 2017, at 4:40 AM, Z Hessam

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

Wait, the file size looks too small. Only 1590 bytes. Did the data get copied properly? Is your drive full? > On Aug 10, 2017, at 4:40 AM, Z Hessam wrote: > > it shows: > > -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

again that error, it shows: 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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

What if you run: freeview -v /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz > On Aug 10, 2017, at 4:40 AM, Z Hessam wrote: > > it shows: > > -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

it shows: -rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesurfer/freesurfer/subjects/bert/mri/T1.mgz On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang wrote: > Hmm, if you run: > > ls -l /media/hessam91/driver2/freesurfer/freesurfer/ >

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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 wrote: > > of course: > > hessam@ubuntu:/media/hessam/driver2/freesurfer/subjects$ freeview -v > bert/mri/T1.mgz

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

$>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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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

Re: [Freesurfer] "failed to load mri" in terminal, not in GUI

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 \

[Freesurfer] "failed to load mri" in terminal, not in GUI

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 \