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.hes...@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 <rpw...@nmr.mgh.harvard.edu > <mailto:rpw...@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.hes...@gmail.com >> <mailto:z.hes...@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 <rpw...@nmr.mgh.harvard.edu >> <mailto:rpw...@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.hes...@gmail.com >>> <mailto: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> . 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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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