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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
> > > > > > > > > > > > 
> > > > > > > > > > > >                                                 
> > > > > > > > > > > > _______________________________________________
> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > > > >                                                 
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> > > > > > > > > >                                     > > > > > > > > > 
> > > > > > > > >                                 > > > > > > > >               
> > > > > > > > >                    
> > > > > > > > 
> > > > > > > >                                     > > > > > > > > > 
> > > > > > > > _______________________________________________
> > > > > > > > >                                     Freesurfer mailing list
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> > > > > > > > >                                     
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> > > > > > > >                             > > > > > > > 
> > > > > > >                         > > > > > > 
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#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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