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 <rpw...@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.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> > 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. 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 >>>>>> >>>>>> >>>>>> 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 >>>>> listfreesur...@nmr.mgh.harvard.eduhttps://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. >>> >>> >> _______________________________________________ >> 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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