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Hi, my concern is the mri_aparc2aseg command line.
In summary, I have done:
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 mri_surf2surf --srcsubject fsaverage5 --trgsubject ADNI001_AD --hemi lh --sval-annot /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/lh.Yeo2011_17Networks_N1000.annot --tval $SUBJECTS_DIR/subj/label/lh.Yeo2011_17Networks_N1000
mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot Yeo2011_17Networks_N1000 --annot-table /Applications/freesurfer/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/fsaverage5/label/rh.Yeo2011_7Networks_N1000.split_components.annot tkmeditfv subj orig.mgz -ov subj/mri/Yeo_17Net.mgz
The output is correct by the color label is those of aparc.
Probably the error is the match between the annotations and annot-table.
Could you check the command lines, please?
Thanks
Stefano
Il 10 marzo 2019 alle 21.15 "Greve, Douglas N.,Ph.D." DGREVE@mgh.harvard.edu ha scritto:
Specify -seg Yeo_17Net.mgz (ie, don't include the full path). I don't know what is in that txt file. You can verify the segids by just bringing up the segmentation in freeview and clicking on a voxel. If you load the segmentation with that color table and everything looks ok, then the color table is ok. On 3/10/19 4:05 PM, stdp82@virgilio.it mailto:stdp82@virgilio.it wrote: > >External Email - Use Caution I will use freeview. Have you any suggestion on the use of fcseed-config option? Are you agree with the command line listed below? fcseed-config -segid ... -seg $SUBJECTS_DIR/subj/mri/Yeo_17Net.mgz -fsd rest -mean -cfg lh.SEED.config -overwrite My concerns are on -segids. Are the ids included in the file 1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt? How can I select a specific seed (id) to be used in -segids? Thanks Stefano > > >Il 10 marzo 2019 alle 17.17 Bruce Fischl <fischl@nmr.mgh.harvard.edu> mailto:fischl@nmr.mgh.harvard.edu ha scritto: 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 mailto:stdp82@virgilio.it wrote: > > > >External Email - Use Caution 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> mailto: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 mailto: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> mailto: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 mailto: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_parcellation/Yeo2011_fcMRI_cluste 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 mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >> >>
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