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 <z.hes...@gmail.com> wrote: > > 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 <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@nmr.mgh.harvard.edu>> wrote: > 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.hes...@gmail.com >> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu >> <mailto:rpw...@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 <fis...@nmr.mgh.harvard.edu >>> <mailto:fis...@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 <fis...@nmr.mgh.harvard.edu >>> <mailto:fis...@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.hes...@gmail.com <mailto:z.hes...@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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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 >>> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <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 >>> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <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 >> <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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > <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 > <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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