External Email - Use Caution 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 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 > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
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