Dear Douglas, To define my new label, I choose the ROI section and choose "New ROI". Then I save it, but it doesn't work properly. In addition, I cant save it on fsaverage.
Best Regards, Mahtab. On 12 May 2016 at 22:08, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > > On 05/12/2016 05:46 AM, Mahtab Farahbakhsh wrote: > > Dear freeSurfer, > > > > I have problems with defining new labels for my brain scan or even of > > fsaverage. I need to define a new label (ROI) to be able to find the > > grey matter thickness for that specific region. > > > > My first problem is that when I define a new label on fsaverage, it > > does not save it for me and it gives me the following error: > > > > > mghRead(/Applications/freesurfer/experimental_data/TG/fsaverage/mri/wm.mgz, > > -1): could not open file > > /Applications/freesurfer/Freeview.app/Contents/MacOS/Freeview: could > > not open label file > > /Applications/freesurfer/subjects/fsaverage/label/ROI_test.label > > > > I intend to define a new label (ROI) on fsaverage and then use the > > mri_labe2label command to copy it on my desired structural MRI image. > > But it does not work for me. > How are you doing this? What tool are you using? What steps with the > tool are you executing? > > > > My second problem is that when I define a new label on my subject's > > MRI image and I run the mri_anatomical_stats with the label of my > > subject, it does not give me any output and this is what I get: > > > > bash-3.2$ mris_anatomical_stats -l anon/label/lh.test.label anon lh > > limiting computations to label anon/label/lh.test.label. > > reading volume > > /Applications/freesurfer/experimental_data/TG//anon/mri/wm.mgz... > > reading input surface > > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... > > reading input pial surface > > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.pial... > > reading input white surface > > /Applications/freesurfer/experimental_data/TG//anon/surf/lh.white... > > > > and the error is that it could not find the file lh.test.label, > > however I can see it in the label folder. > Use the -b or -f flags to specify an output > > > > Please guide me with this issue. > > > > Best Regards, > > Mahtab. > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > 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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