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> wrote: > How did you put the data on your drive? > > On Aug 10, 2017, at 9:25 AM, Z Hessam <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> > 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> 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 <rpw...@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.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/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 < >>> 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> 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> >>>>>> 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> 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. 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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 >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> >> _______________________________________________ >> 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 > > > > _______________________________________________ > 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. > >
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