External Email - Use Caution Hi Stefano,
Sorry. Can you confirm left hemisphere is ok? I think in this version of the annot file, the right hemisphere regions will start off as 2058, rather than 2001. So instead of numbering from 2001 to 2057, it should be from 2058 to 2114. Sorry about that. There are some intricacies between the annot format and mri_aparc2aseg that we were not aware of. We are trying to fix the issue now, but not so soon. Regards, Thomas On Wed, Mar 27, 2019 at 6:14 PM <std...@virgilio.it> wrote: > I have renumbered and run: > > mri_aparc2aseg --s subj --o subj/mri/Yeo_17Net.mgz --annot > Yeo2011_17Networks_N1000 --annot-table Yeo2011_17Networks_renumbered.txt > When I open the Yeo_17Net.mgz in freeview, the PCC portion of the DMN > "2016 is visualized but labeled as rh_parahippocampal. > > What's happened? > > Thanks > > Best regards, > > Stefano > > Il 26 marzo 2019 alle 13.05 Thomas Yeo <ytho...@csail.mit.edu> ha > scritto: > > External Email - Use Caution > > > Renumber for visualization purpose. > > Do you mean how to re-number in the colortable? Just open the colortable > in a text editing software and edit. > > Thanks, > Thomas > > On Tue, Mar 26, 2019 at 6:44 PM < std...@virgilio.it> wrote: > > Thanks. > > Should I renumber for visualization purpose or for fs-fast? > > How can I do it? > > > Il 26 marzo 2019 alle 4.01 Thomas Yeo < ytho...@csail.mit.edu> ha > scritto: > > Hi Stefano, > > Can I confirm that in Yeo_17Net.mgz, the left hemisphere parcels are 1001, > 1002 to 1057? And the right hemisphere parcels are 2001, 2002, to 2057? > > If so, you will just need the right colortable to view the Yeo_17Net.mgz. > We are currently generating a new colortable that should work for you. This > might take a while. > > If you are in a hurry, you can download the colortable here ( > https://github.com/ThomasYeoLab/CBIG/blob/master/stable_projects/brain_parcellation/Yeo2011_fcMRI_clustering/1000subjects_reference/Yeo_JNeurophysiol11_SplitLabels/MNI152/17Networks_ColorLUT_freeview.txt), > but as you can see the range of values are not in the 1000-2000 range. So > what you need to do is for the left hemisphere structures, you need to > renumber them from 1 to 57 to 1001 to 1057. For the right hemisphere > structures, you need to renumber them from 58 to 114 to 2001 to 2057. > > Regards, > Thomas > > On Sun, Mar 24, 2019 at 12:18 AM < std...@virgilio.it> wrote: > > 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." < > dgr...@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, std...@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 <fis...@nmr.mgh.harvard.edu> > <fis...@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, std...@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 <ytho...@csail.mit.edu> > <ytho...@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 < std...@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." > <dgr...@mgh.harvard.edu> <dgr...@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, std...@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 > 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 > > _______________________________________________ > 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 > > _______________________________________________ > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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