External Email - Use Caution Please see the attached file.
> Il 27 marzo 2019 alle 15.39 Thomas Yeo <ytho...@csail.mit.edu> ha scritto: > > > External Email - Use Caution > > > > Hi Stefano, > > Can you attach your updated colortable, so we can take a look? > > Thanks, > Thomas > > On Wed, Mar 27, 2019 at 10:27 PM < std...@virgilio.it > mailto:std...@virgilio.it > wrote: > > > > > > 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 mailto: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 > > > 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 >
#No. Label Name: R G B A 0 Unknown 0 0 0 0 1 Left-Cerebral-Exterior 70 130 180 0 2 Left-Cerebral-White-Matter 245 245 245 0 3 Left-Cerebral-Cortex 205 62 78 0 4 Left-Lateral-Ventricle 120 18 134 0 5 Left-Inf-Lat-Vent 196 58 250 0 6 Left-Cerebellum-Exterior 0 148 0 0 7 Left-Cerebellum-White-Matter 220 248 164 0 8 Left-Cerebellum-Cortex 230 148 34 0 9 Left-Thalamus 0 118 14 0 10 Left-Thalamus-Proper 0 118 14 0 11 Left-Caudate 122 186 220 0 12 Left-Putamen 236 13 176 0 13 Left-Pallidum 12 48 255 0 14 3rd-Ventricle 204 182 142 0 15 4th-Ventricle 42 204 164 0 16 Brain-Stem 119 159 176 0 17 Left-Hippocampus 220 216 20 0 18 Left-Amygdala 103 255 255 0 19 Left-Insula 80 196 98 0 20 Left-Operculum 60 58 210 0 21 Line-1 60 58 210 0 22 Line-2 60 58 210 0 23 Line-3 60 58 210 0 24 CSF 60 60 60 0 25 Left-Lesion 255 165 0 0 26 Left-Accumbens-area 255 165 0 0 27 Left-Substancia-Nigra 0 255 127 0 28 Left-VentralDC 165 42 42 0 29 Left-undetermined 135 206 235 0 30 Left-vessel 160 32 240 0 31 Left-choroid-plexus 0 200 200 0 32 Left-F3orb 100 50 100 0 33 Left-lOg 135 50 74 0 34 Left-aOg 122 135 50 0 35 Left-mOg 51 50 135 0 36 Left-pOg 74 155 60 0 37 Left-Stellate 120 62 43 0 38 Left-Porg 74 155 60 0 39 Left-Aorg 122 135 50 0 40 Right-Cerebral-Exterior 70 130 180 0 41 Right-Cerebral-White-Matter 245 245 245 0 42 Right-Cerebral-Cortex 205 62 78 0 43 Right-Lateral-Ventricle 120 18 134 0 44 Right-Inf-Lat-Vent 196 58 250 0 45 Right-Cerebellum-Exterior 0 148 0 0 46 Right-Cerebellum-White-Matter 220 248 164 0 47 Right-Cerebellum-Cortex 230 148 34 0 48 Right-Thalamus 0 118 14 0 49 Right-Thalamus-Proper 0 118 14 0 50 Right-Caudate 122 186 220 0 51 Right-Putamen 236 13 176 0 52 Right-Pallidum 13 48 255 0 53 Right-Hippocampus 220 216 20 0 54 Right-Amygdala 103 255 255 0 55 Right-Insula 80 196 98 0 56 Right-Operculum 60 58 210 0 57 Right-Lesion 255 165 0 0 58 Right-Accumbens-area 255 165 0 0 59 Right-Substancia-Nigra 0 255 127 0 60 Right-VentralDC 165 42 42 0 61 Right-undetermined 135 206 235 0 62 Right-vessel 160 32 240 0 63 Right-choroid-plexus 0 200 221 0 64 Right-F3orb 100 50 100 0 65 Right-lOg 135 50 74 0 66 Right-aOg 122 135 50 0 67 Right-mOg 51 50 135 0 68 Right-pOg 74 155 60 0 69 Right-Stellate 120 62 43 0 70 Right-Porg 74 155 60 0 71 Right-Aorg 122 135 50 0 72 5th-Ventricle 120 190 150 0 73 Left-Interior 122 135 50 0 74 Right-Interior 122 135 50 0 # 75/76 removed. duplicates of 4/43 77 WM-hypointensities 200 70 255 0 78 Left-WM-hypointensities 255 148 10 0 79 Right-WM-hypointensities 255 148 10 0 80 non-WM-hypointensities 164 108 226 0 81 Left-non-WM-hypointensities 164 108 226 0 82 Right-non-WM-hypointensities 164 108 226 0 83 Left-F1 255 218 185 0 84 Right-F1 255 218 185 0 85 Optic-Chiasm 234 169 30 0 192 Corpus_Callosum 250 255 50 0 86 Left_future_WMSA 200 120 255 0 87 Right_future_WMSA 200 121 255 0 88 future_WMSA 200 122 255 0 96 Left-Amygdala-Anterior 205 10 125 0 97 Right-Amygdala-Anterior 205 10 125 0 98 Dura 160 32 240 0 100 Left-wm-intensity-abnormality 124 140 178 0 101 Left-caudate-intensity-abnormality 125 140 178 0 102 Left-putamen-intensity-abnormality 126 140 178 0 103 Left-accumbens-intensity-abnormality 127 140 178 0 104 Left-pallidum-intensity-abnormality 124 141 178 0 105 Left-amygdala-intensity-abnormality 124 142 178 0 106 Left-hippocampus-intensity-abnormality 124 143 178 0 107 Left-thalamus-intensity-abnormality 124 144 178 0 108 Left-VDC-intensity-abnormality 124 140 179 0 109 Right-wm-intensity-abnormality 124 140 178 0 110 Right-caudate-intensity-abnormality 125 140 178 0 111 Right-putamen-intensity-abnormality 126 140 178 0 112 Right-accumbens-intensity-abnormality 127 140 178 0 113 Right-pallidum-intensity-abnormality 124 141 178 0 114 Right-amygdala-intensity-abnormality 124 142 178 0 115 Right-hippocampus-intensity-abnormality 124 143 178 0 116 Right-thalamus-intensity-abnormality 124 144 178 0 117 Right-VDC-intensity-abnormality 124 140 179 0 118 Epidermis 255 20 147 0 119 Conn-Tissue 205 179 139 0 120 SC-Fat-Muscle 238 238 209 0 121 Cranium 200 200 200 0 122 CSF-SA 74 255 74 0 123 Muscle 238 0 0 0 124 Ear 0 0 139 0 125 Adipose 173 255 47 0 126 Spinal-Cord 133 203 229 0 127 Soft-Tissue 26 237 57 0 128 Nerve 34 139 34 0 129 Bone 30 144 255 0 130 Air 147 19 173 0 131 Orbital-Fat 238 59 59 0 132 Tongue 221 39 200 0 133 Nasal-Structures 238 174 238 0 134 Globe 255 0 0 0 135 Teeth 72 61 139 0 136 Left-Caudate-Putamen 21 39 132 0 137 Right-Caudate-Putamen 21 39 132 0 138 Left-Claustrum 65 135 20 0 139 Right-Claustrum 65 135 20 0 140 Cornea 134 4 160 0 142 Diploe 221 226 68 0 143 Vitreous-Humor 255 255 254 0 144 Lens 52 209 226 0 145 Aqueous-Humor 239 160 223 0 146 Outer-Table 70 130 180 0 147 Inner-Table 70 130 181 0 148 Periosteum 139 121 94 0 149 Endosteum 224 224 224 0 150 R-C-S 255 0 0 0 151 Iris 205 205 0 0 152 SC-Adipose-Muscle 238 238 209 0 153 SC-Tissue 139 121 94 0 154 Orbital-Adipose 238 59 59 0 155 Left-IntCapsule-Ant 238 59 59 0 156 Right-IntCapsule-Ant 238 59 59 0 157 Left-IntCapsule-Pos 62 10 205 0 158 Right-IntCapsule-Pos 62 10 205 0 # These labels are for babies/children 159 Left-Cerebral-WM-unmyelinated 0 118 14 0 160 Right-Cerebral-WM-unmyelinated 0 118 14 0 161 Left-Cerebral-WM-myelinated 220 216 21 0 162 Right-Cerebral-WM-myelinated 220 216 21 0 163 Left-Subcortical-Gray-Matter 122 186 220 0 164 Right-Subcortical-Gray-Matter 122 186 220 0 165 Skull 120 120 120 0 166 Posterior-fossa 14 48 255 0 167 Scalp 166 42 42 0 168 Hematoma 121 18 134 0 169 Left-Basal-Ganglia 236 13 127 0 176 Right-Basal-Ganglia 236 13 126 0 # Label names and colors for Brainstem consituents # No. Label Name: R G B A 170 brainstem 119 159 176 0 171 DCG 119 0 176 0 172 Vermis 119 100 176 0 173 Midbrain 242 104 76 0 174 Pons 206 195 58 0 175 Medulla 119 159 176 0 177 Vermis-White-Matter 119 50 176 0 178 SCP 142 182 0 0 179 Floculus 19 100 176 0 #176 Right-Basal-Ganglia found in babies/children section above 180 Left-Cortical-Dysplasia 73 61 139 0 181 Right-Cortical-Dysplasia 73 62 139 0 182 CblumNodulus 10 100 176 0 #192 Corpus_Callosum listed after #85 above 193 Left-hippocampal_fissure 0 196 255 0 194 Left-CADG-head 255 164 164 0 195 Left-subiculum 196 196 0 0 196 Left-fimbria 0 100 255 0 197 Right-hippocampal_fissure 128 196 164 0 198 Right-CADG-head 0 126 75 0 199 Right-subiculum 128 96 64 0 200 Right-fimbria 0 50 128 0 201 alveus 255 204 153 0 202 perforant_pathway 255 128 128 0 203 parasubiculum 255 255 0 0 204 presubiculum 64 0 64 0 205 subiculum 0 0 255 0 206 CA1 255 0 0 0 207 CA2 128 128 255 0 208 CA3 0 128 0 0 209 CA4 196 160 128 0 210 GC-DG 32 200 255 0 211 HATA 128 255 128 0 212 fimbria 204 153 204 0 213 lateral_ventricle 121 17 136 0 214 molecular_layer_HP 128 0 0 0 215 hippocampal_fissure 128 32 255 0 216 entorhinal_cortex 255 204 102 0 217 molecular_layer_subiculum 128 128 128 0 218 Amygdala 104 255 255 0 219 Cerebral_White_Matter 0 226 0 0 220 Cerebral_Cortex 205 63 78 0 221 Inf_Lat_Vent 197 58 250 0 222 Perirhinal 33 150 250 0 223 Cerebral_White_Matter_Edge 226 0 0 0 224 Background 100 100 100 0 225 Ectorhinal 197 150 250 0 226 HP_tail 170 170 255 0 250 Fornix 255 0 0 0 251 CC_Posterior 0 0 64 0 252 CC_Mid_Posterior 0 0 112 0 253 CC_Central 0 0 160 0 254 CC_Mid_Anterior 0 0 208 0 255 CC_Anterior 0 0 255 0 # This is for keeping track of voxel changes 256 Voxel-Unchanged 0 0 0 0 257 CSF-ExtraCerebral 60 60 60 0 258 Head-ExtraCerebral 150 150 200 0 259 SkullApprox 120 120 120 0 260 BoneOrAir 119 159 176 0 261 PossibleFluid 120 18 134 0 262 Sinus 119 159 176 0 263 Left-Eustachian 119 159 176 0 264 Right-Eustachian 119 159 176 0 # lymph node and vascular labels 331 Aorta 255 0 0 0 332 Left-Common-IliacA 255 80 0 0 333 Right-Common-IliacA 255 160 0 0 334 Left-External-IliacA 255 255 0 0 335 Right-External-IliacA 0 255 0 0 336 Left-Internal-IliacA 255 0 160 0 337 Right-Internal-IliacA 255 0 255 0 338 Left-Lateral-SacralA 255 50 80 0 339 Right-Lateral-SacralA 80 255 50 0 340 Left-ObturatorA 160 255 50 0 341 Right-ObturatorA 160 200 255 0 342 Left-Internal-PudendalA 0 255 160 0 343 Right-Internal-PudendalA 0 0 255 0 344 Left-UmbilicalA 80 50 255 0 345 Right-UmbilicalA 160 0 255 0 346 Left-Inf-RectalA 255 210 0 0 347 Right-Inf-RectalA 0 160 255 0 348 Left-Common-IliacV 255 200 80 0 349 Right-Common-IliacV 255 200 160 0 350 Left-External-IliacV 255 80 200 0 351 Right-External-IliacV 255 160 200 0 352 Left-Internal-IliacV 30 255 80 0 353 Right-Internal-IliacV 80 200 255 0 354 Left-ObturatorV 80 255 200 0 355 Right-ObturatorV 195 255 200 0 356 Left-Internal-PudendalV 120 200 20 0 357 Right-Internal-PudendalV 170 10 200 0 358 Pos-Lymph 20 130 180 0 359 Neg-Lymph 20 180 130 0 400 V1 206 62 78 0 401 V2 121 18 134 0 402 BA44 199 58 250 0 403 BA45 1 148 0 0 404 BA4a 221 248 164 0 405 BA4p 231 148 34 0 406 BA6 1 118 14 0 407 BA2 120 118 14 0 408 BA1_old 123 186 221 0 409 BAun2 238 13 177 0 410 BA1 123 186 220 0 411 BA2b 138 13 206 0 412 BA3a 238 130 176 0 413 BA3b 218 230 76 0 414 MT 38 213 176 0 415 AIPS_AIP_l 1 225 176 0 416 AIPS_AIP_r 1 225 176 0 417 AIPS_VIP_l 200 2 100 0 418 AIPS_VIP_r 200 2 100 0 419 IPL_PFcm_l 5 200 90 0 420 IPL_PFcm_r 5 200 90 0 421 IPL_PF_l 100 5 200 0 422 IPL_PFm_l 25 255 100 0 423 IPL_PFm_r 25 255 100 0 424 IPL_PFop_l 230 7 100 0 425 IPL_PFop_r 230 7 100 0 426 IPL_PF_r 100 5 200 0 427 IPL_PFt_l 150 10 200 0 428 IPL_PFt_r 150 10 200 0 429 IPL_PGa_l 175 10 176 0 430 IPL_PGa_r 175 10 176 0 431 IPL_PGp_l 10 100 255 0 432 IPL_PGp_r 10 100 255 0 433 Visual_V3d_l 150 45 70 0 434 Visual_V3d_r 150 45 70 0 435 Visual_V4_l 45 200 15 0 436 Visual_V4_r 45 200 15 0 437 Visual_V5_b 227 45 100 0 438 Visual_VP_l 227 45 100 0 439 Visual_VP_r 227 45 100 0 # wm lesions 498 wmsa 143 188 143 0 499 other_wmsa 255 248 220 0 # HiRes Hippocampus labeling 500 right_CA2_3 17 85 136 0 501 right_alveus 119 187 102 0 502 right_CA1 204 68 34 0 503 right_fimbria 204 0 255 0 504 right_presubiculum 221 187 17 0 505 right_hippocampal_fissure 153 221 238 0 506 right_CA4_DG 51 17 17 0 507 right_subiculum 0 119 85 0 508 right_fornix 20 100 200 0 550 left_CA2_3 17 85 137 0 551 left_alveus 119 187 103 0 552 left_CA1 204 68 35 0 553 left_fimbria 204 0 254 0 554 left_presubiculum 221 187 16 0 555 left_hippocampal_fissure 153 221 239 0 556 left_CA4_DG 51 17 18 0 557 left_subiculum 0 119 86 0 558 left_fornix 20 100 201 0 600 Tumor 254 254 254 0 # Cerebellar parcellation labels from SUIT (matches labels in cma.h) #No. Label Name: R G B A 601 Cbm_Left_I_IV 70 130 180 0 602 Cbm_Right_I_IV 245 245 245 0 603 Cbm_Left_V 205 62 78 0 604 Cbm_Right_V 120 18 134 0 605 Cbm_Left_VI 196 58 250 0 606 Cbm_Vermis_VI 0 148 0 0 607 Cbm_Right_VI 220 248 164 0 608 Cbm_Left_CrusI 230 148 34 0 609 Cbm_Vermis_CrusI 0 118 14 0 610 Cbm_Right_CrusI 0 118 14 0 611 Cbm_Left_CrusII 122 186 220 0 612 Cbm_Vermis_CrusII 236 13 176 0 613 Cbm_Right_CrusII 12 48 255 0 614 Cbm_Left_VIIb 204 182 142 0 615 Cbm_Vermis_VIIb 42 204 164 0 616 Cbm_Right_VIIb 119 159 176 0 617 Cbm_Left_VIIIa 220 216 20 0 618 Cbm_Vermis_VIIIa 103 255 255 0 619 Cbm_Right_VIIIa 80 196 98 0 620 Cbm_Left_VIIIb 60 58 210 0 621 Cbm_Vermis_VIIIb 60 58 210 0 622 Cbm_Right_VIIIb 60 58 210 0 623 Cbm_Left_IX 60 58 210 0 624 Cbm_Vermis_IX 60 60 60 0 625 Cbm_Right_IX 255 165 0 0 626 Cbm_Left_X 255 165 0 0 627 Cbm_Vermis_X 0 255 127 0 628 Cbm_Right_X 165 42 42 0 # Cerebellar lobule parcellations 640 Cbm_Right_I_V_med 204 0 0 0 641 Cbm_Right_I_V_mid 255 0 0 0 642 Cbm_Right_VI_med 0 0 255 0 643 Cbm_Right_VI_mid 30 144 255 0 644 Cbm_Right_VI_lat 100 212 237 0 645 Cbm_Right_CrusI_med 218 165 32 0 646 Cbm_Right_CrusI_mid 255 215 0 0 647 Cbm_Right_CrusI_lat 255 255 166 0 648 Cbm_Right_CrusII_med 153 0 204 0 649 Cbm_Right_CrusII_mid 153 141 209 0 650 Cbm_Right_CrusII_lat 204 204 255 0 651 Cbm_Right_7med 31 212 194 0 652 Cbm_Right_7mid 3 255 237 0 653 Cbm_Right_7lat 204 255 255 0 654 Cbm_Right_8med 86 74 147 0 655 Cbm_Right_8mid 114 114 190 0 656 Cbm_Right_8lat 184 178 255 0 657 Cbm_Right_PUNs 126 138 37 0 658 Cbm_Right_TONs 189 197 117 0 659 Cbm_Right_FLOs 240 230 140 0 660 Cbm_Left_I_V_med 204 0 0 0 661 Cbm_Left_I_V_mid 255 0 0 0 662 Cbm_Left_VI_med 0 0 255 0 663 Cbm_Left_VI_mid 30 144 255 0 664 Cbm_Left_VI_lat 100 212 237 0 665 Cbm_Left_CrusI_med 218 165 32 0 666 Cbm_Left_CrusI_mid 255 215 0 0 667 Cbm_Left_CrusI_lat 255 255 166 0 668 Cbm_Left_CrusII_med 153 0 204 0 669 Cbm_Left_CrusII_mid 153 141 209 0 670 Cbm_Left_CrusII_lat 204 204 255 0 671 Cbm_Left_7med 31 212 194 0 672 Cbm_Left_7mid 3 255 237 0 673 Cbm_Left_7lat 204 255 255 0 674 Cbm_Left_8med 86 74 147 0 675 Cbm_Left_8mid 114 114 190 0 676 Cbm_Left_8lat 184 178 255 0 677 Cbm_Left_PUNs 126 138 37 0 678 Cbm_Left_TONs 189 197 117 0 679 Cbm_Left_FLOs 240 230 140 0 # Added by DNG 7/31/14 690 CbmWM_Gyri_Left 122 135 50 0 691 CbmWM_Gyri_Right 122 135 50 0 701 CSF-FSL-FAST 120 18 134 0 702 GrayMatter-FSL-FAST 205 62 78 0 703 WhiteMatter-FSL-FAST 0 225 0 0 999 SUSPICIOUS 255 100 100 0 1000 FreeSurfer_Defined_Medial_Wall 1 1 1 0 1001 17Networks_LH_VisCent_Striate 120 18 134 0 1002 17Networks_LH_VisCent_ExStr 120 18 135 0 1003 17Networks_LH_VisPeri_Striate 255 0 0 0 1004 17Networks_LH_VisPeri_ExStrInf 255 0 1 0 1005 17Networks_LH_VisPeri_ExStrSup 255 1 0 0 1006 17Networks_LH_SomMotA 70 130 180 0 1007 17Networks_LH_SomMotB_Cent 42 204 164 0 1008 17Networks_LH_SomMotB_S2 42 204 165 0 1009 17Networks_LH_SomMotB_Ins 42 205 165 0 1010 17Networks_LH_SomMotB_Aud 43 204 164 0 1011 17Networks_LH_DorsAttnA_TempOcc 74 155 60 0 1012 17Networks_LH_DorsAttnA_ParOcc 74 155 61 0 1013 17Networks_LH_DorsAttnA_SPL 74 156 60 0 1014 17Networks_LH_DorsAttnB_TempOcc 0 118 14 0 1015 17Networks_LH_DorsAttnB_PostC 0 118 15 0 1016 17Networks_LH_DorsAttnB_FEF 0 119 14 0 1017 17Networks_LH_DorsAttnB_PrCv 0 119 15 0 1018 17Networks_LH_SalVentAttnA_ParOper 196 58 250 0 1019 17Networks_LH_SalVentAttnA_PrCv 196 58 251 0 1020 17Networks_LH_SalVentAttnA_Ins 196 59 250 0 1021 17Networks_LH_SalVentAttnA_ParMed 196 59 251 0 1022 17Networks_LH_SalVentAttnA_FrMed 197 58 250 0 1023 17Networks_LH_SalVentAttnB_IPL 255 152 213 0 1024 17Networks_LH_SalVentAttnB_PFCd 255 152 214 0 1025 17Networks_LH_SalVentAttnB_PFCl 255 153 213 0 1026 17Networks_LH_SalVentAttnB_PFCv 255 153 214 0 1027 17Networks_LH_SalVentAttnB_OFC 255 152 212 0 1028 17Networks_LH_SalVentAttnB_PFCmp 255 151 213 0 1029 17Networks_LH_Limbic_TempPole 220 248 164 0 1030 17Networks_LH_Limbic_OFC 122 135 50 0 1031 17Networks_LH_ContA_Temp 230 148 34 0 1032 17Networks_LH_ContA_IPS 230 148 35 0 1033 17Networks_LH_ContA_PFCd 230 149 34 0 1034 17Networks_LH_ContA_PFCl 230 149 35 0 1035 17Networks_LH_ContA_PFClv 231 148 34 0 1036 17Networks_LH_ContA_Cinga 231 148 35 0 1037 17Networks_LH_ContB_Temp 135 50 74 0 1038 17Networks_LH_ContB_IPL 135 50 75 0 1039 17Networks_LH_ContB_PFCd 135 51 74 0 1040 17Networks_LH_ContB_PFCl 135 51 75 0 1041 17Networks_LH_ContB_PFClv 136 50 74 0 1042 17Networks_LH_ContB_PFCmp 136 50 75 0 1043 17Networks_LH_ContC_pCun 119 140 176 0 1044 17Networks_LH_ContC_Cingp 119 140 177 0 1045 17Networks_LH_DefaultA_IPL 255 255 0 0 1046 17Networks_LH_DefaultA_PFCd 255 255 1 0 1047 17Networks_LH_DefaultA_PCC 255 254 0 0 1048 17Networks_LH_DefaultA_PFCm 254 255 0 0 1049 17Networks_LH_DefaultB_Temp 205 62 78 0 1050 17Networks_LH_DefaultB_IPL 205 62 79 0 1051 17Networks_LH_DefaultB_PFCd 205 63 78 0 1052 17Networks_LH_DefaultB_PFCl 205 63 79 0 1053 17Networks_LH_DefaultB_PFCv 206 62 78 0 1054 17Networks_LH_DefaultC_IPL 0 0 130 0 1055 17Networks_LH_DefaultC_Rsp 0 0 131 0 1056 17Networks_LH_DefaultC_PHC 0 1 130 0 1057 17Networks_LH_TempPar 12 48 255 0 2000 FreeSurfer_Defined_Medial_Wall 1 1 1 0 2058 17Networks_RH_VisCent_Striate 120 18 134 0 2059 17Networks_RH_VisCent_ExStr 120 18 135 0 2060 17Networks_RH_VisPeri_Striate 255 0 0 0 2061 17Networks_RH_VisPeri_ExStrInf 255 0 1 0 2062 17Networks_RH_VisPeri_ExStrSup 255 1 0 0 2063 17Networks_RH_SomMotA 70 130 180 0 2064 17Networks_RH_SomMotB_Cent 42 204 164 0 2065 17Networks_RH_SomMotB_S2 42 204 165 0 2066 17Networks_RH_SomMotB_Ins 42 205 165 0 2067 17Networks_RH_SomMotB_Aud 43 204 164 0 2068 17Networks_RH_DorsAttnA_TempOcc 74 155 60 0 2069 17Networks_RH_DorsAttnA_ParOcc 74 155 61 0 2070 17Networks_RH_DorsAttnA_SPL 74 156 60 0 2071 17Networks_RH_DorsAttnB_TempOcc 0 118 14 0 2072 17Networks_RH_DorsAttnB_PostC 0 118 15 0 2073 17Networks_RH_DorsAttnB_FEF 0 119 14 0 2074 17Networks_RH_DorsAttnB_PrCv 0 119 15 0 2075 17Networks_RH_SalVentAttnA_ParOper 196 58 250 0 2076 17Networks_RH_SalVentAttnA_PrC 196 58 251 0 2077 17Networks_RH_SalVentAttnA_PrCv 196 59 250 0 2078 17Networks_RH_SalVentAttnA_Ins 196 59 251 0 2079 17Networks_RH_SalVentAttnA_ParMed 197 58 250 0 2080 17Networks_RH_SalVentAttnA_FrMed 255 152 213 0 2081 17Networks_RH_SalVentAttnB_IPL 255 152 214 0 2082 17Networks_RH_SalVentAttnB_PFCd 255 153 213 0 2083 17Networks_RH_SalVentAttnB_PFCl 255 153 214 0 2084 17Networks_RH_SalVentAttnB_PFClv 255 152 212 0 2085 17Networks_RH_SalVentAttnB_PFCv 255 151 213 0 2086 17Networks_RH_SalVentAttnB_PFCmp 220 248 164 0 2087 17Networks_RH_SalVentAttnB_Cinga 122 135 50 0 2088 17Networks_RH_Limbic_TempPole 230 148 34 0 2089 17Networks_RH_Limbic_OFC 230 148 35 0 2090 17Networks_RH_ContA_Temp 230 149 34 0 2091 17Networks_RH_ContA_IPS 230 149 35 0 2092 17Networks_RH_ContA_PFCd 231 148 34 0 2093 17Networks_RH_ContA_PFCl 231 148 35 0 2094 17Networks_RH_ContA_Cinga 135 50 74 0 2095 17Networks_RH_ContB_Temp 135 50 75 0 2096 17Networks_RH_ContB_IPL 135 51 74 0 2097 17Networks_RH_ContB_PFCld 135 51 75 0 2098 17Networks_RH_ContB_PFClv 136 50 74 0 2099 17Networks_RH_ContB_PFCmp 136 50 75 0 2100 17Networks_RH_ContC_pCun 119 140 176 0 2101 17Networks_RH_ContC_Cingp 119 140 177 0 2102 17Networks_RH_DefaultA_Temp 255 255 0 0 2103 17Networks_RH_DefaultA_IPL 255 255 1 0 2104 17Networks_RH_DefaultA_PFCd 255 254 0 0 2105 17Networks_RH_DefaultA_PCC 254 255 0 0 2106 17Networks_RH_DefaultA_PFCm 205 62 78 0 2107 17Networks_RH_DefaultB_Temp 205 62 79 0 2108 17Networks_RH_DefaultB_AntTemp 205 63 78 0 2109 17Networks_RH_DefaultB_PFCd 205 63 79 0 2110 17Networks_RH_DefaultB_PFCv 206 62 78 0 2111 17Networks_RH_DefaultC_IPL 0 0 130 0 2112 17Networks_RH_DefaultC_Rsp 0 0 131 0 2113 17Networks_RH_DefaultC_PHC 0 1 130 0 2114 17Networks_RH_TempPar 12 48 255 0
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