External Email - Use Caution Yes the left hemisphere is fine.
The error occurs again. The labels for posterior DMN and anterior DMN are the same and numbered like 1016 and 2016, despite I have modified the txt. Thanks Stefano > Il 27 marzo 2019 alle 13.09 Thomas Yeo <ytho...@csail.mit.edu> ha scritto: > > > 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 > mailto: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 mailto: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 > > > mailto: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 mailto: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 mailto: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 > > > > > > mailto: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 mailto: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> > > > > > > > > > mailto: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 mailto: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> > > > > > > > > > > mailto: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 mailto: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> mailto: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 mailto: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 > > > > > > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > > _______________________________________________ > > > > > > > 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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