Hi Stefano
is there a reason you are using tkmedit and not freeview? We deprecated tkmedit a long time ago now
cheers Bruce On Sun, 10 Mar 2019, stdp82@virgilio.it wrote:
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Thanks.
My error is in tkmedit
tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
Il 9 marzo 2019 alle 11.09 Thomas Yeo <ythomas@csail.mit.edu> ha scritto: External Email - Use Caution Just to clarify, rh.Yeo2011_17Networks_N1000.annot looks fine, but Yeo_17Net.mgz is empty?Your tkmedit command seems to assume Yeo_17Net.mgz is in /Applications/freesurfer/subjects/subject_prova/. But shouldn't the output be in the mri folder?
On Sat, Mar 9, 2019 at 5:47 PM < stdp82@virgilio.it> wrote:
External Email - Use Caution I have run: mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo20 11_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000 to check the output tksurfer subj rh inflated -annot $SUBJECTS_DIR/subj/label/rh.Yeo2011_17Networks_N1000.annot My concern is here: mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table/Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLU T_freeview.txt --sval-annot yeoData_fsaverage5/rh.Yeo2011_17Networks_N1000.split_components.annot tkmeditfv fsaverage orig.mgz -ov /Applications/freesurfer/subjects/subject_prova/Yeo_17Net.mgz Yeo_17Net.mgz is empty. Stefano Il 7 marzo 2019 alle 23.57 "Greve, Douglas N.,Ph.D." <DGREVE@mgh.harvard.edu> ha scritto: You have to convert the annotation to a volume using mri_aparc2aseg (look at recon-all.log for an example, but note that you'll need to specify the output so that it does not overwrite). You'll then need to look in the output segmentation and see what the segmentation ids are On 3/7/19 4:13 PM, stdp82@virgilio.it wrote: > External Email - Use Caution Hi list, I'd like to use the regions included in Yeo 17 networks(https://github.com/ThomasYeoLab/CBIG/tree/master/stable_projects/brain_parce... ring).
in FS-FAST. Which is the command line to be used to create a segmentation in $SUBJECTS_DIR/$subject/mri in the same format as aseg.mgz? (I'd like to use it to run fcseed-config, specify -seg yourseg.mgz -segid). Thanks Stefano _______________________________________________ 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
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