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 rpwang@nmr.mgh.harvard.edu 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 file was not properly written...
On Aug 10, 2017, at 9:34 AM, Z Hessam z.hessam@gmail.com wrote:
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 -subjid fat_fh23" command to *.mgz, and then i use the "recon-all -s .... -all " command in linux terminal.
On Thu, Aug 10, 2017 at 5:56 PM, Ruopeng Wang rpwang@nmr.mgh.harvard.edu wrote:
How did you put the data on your drive?
On Aug 10, 2017, at 9:25 AM, Z Hessam z.hessam@gmail.com 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 <rpwang@nmr.mgh.harvard.edu
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 z.hessam@gmail.com wrote:
it shows:
-rwxrwxrwx 1 8481 1590 0 Aug 9 22:30 /media/hessam91/driver2/freesu rfer/freesurfer/subjects/bert/mri/T1.mgz
On Thu, Aug 10, 2017 at 2:55 AM, Ruopeng Wang < rpwang@nmr.mgh.harvard.edu> wrote:
Hmm, if you run:
ls -l /media/hessam91/driver2/freesurfer/freesurfer/subjects/be rt/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/freesu rfer/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/freesu rfer/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> 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> 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> > 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 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to > whom > it is > addressed. If you believe this e-mail was sent to you in error and > the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to > you > in error > but does not contain patient information, please contact the sender > and properly > dispose of the e-mail. > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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