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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 > 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 > > > > > > > > > > > > >
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