Dear freeSurfer, Thank you. I can use mris_anatomical_stats for the labels that are already defined, but when I want to define a new label, it does not work.
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. 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. Please guide me with this issue. Best Regards, Mahtab. On 6 May 2016 at 16:45, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > If you have a label, then you can use mris_anatomical_stats with the -l > option > doug > > On 05/06/2016 10:01 AM, Mahtab Farahbakhsh wrote: > > Dear FreeSurfer, > > > > I am trying to find the cortical thickness of my ROI which is the > > perisylvian region of the left hemisphere. What I did was to define a > > label based on the anatomical area of this region and tried to define > > a ROI based on this label and the command -mri_label2volume. Howevere, > > I am using freeview and the tutorial that I found about this issue was > > based on tkmedit. Would you please guide me how I should get this done? > > > > Best Regards, > > Mahtab Farahbakhsh. > > > > > > > > _______________________________________________ > > 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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