External Email - Use Caution Hi Stefano,
How are you using the colortable? Are you just passing it as a flag to mri_aparc2aseg? As far as I know (and I am NOT very knowledgeable, so I could be wrong), the volumetric file (Yeo_17Net.mgz) does not contain the color information. So when I said you should use the colortable, I meant you should use it with the viewer. I am not sure about tkmedit, but for freeview, you can load your volume and then also load your own colortable. Regards, Thomas On Wed, Mar 27, 2019 at 11:13 PM <std...@virgilio.it> wrote: > The problem persists. > > We are sure that the command lines which I'm using are corrected? > > 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 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 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/MNI152/Yeo2011_17network_SplitLabels_LUT_rh2058.txt > > > Il 27 marzo 2019 alle 15.40 Aihuiping Xue <xueaihuip...@gmail.com> ha > scritto: > > Hi Stefano, > > I created a lookup table for your case. You can load your .mgz file and > try this lookup table in freeview. > > This is a temporary solution. We will modify the annot files and provide > another version of lookup table. But that will take some time. I hope this > lookup table can solve your problem for now. > > Best Regards, > XUE Aihuiping > > < std...@virgilio.it> 于2019年3月27日周三 下午10:26写道： > > 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> 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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >
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