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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 CautionI have run:
mri_surf2surf --srcsubject fsaverage5 --trgsubject subj--hemi rh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_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_ColorLUT_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:
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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... ).
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
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