Use mris_anatomical_stats to create an LUT with the -c option. You can look in recon-all.cmd for an example. You only need to do one hemi as they both will be the same.
There are four sections of the new LUT: lh cortex, rh cortex, lh WM, and rh WM. For each one, you replicate the LUT created above but change the index number (first column) by adding a constant: 1000, 2000, 3000, 4000. You can also change the name to indicate the hemi and tissue type. Look in  $FREESURFER_HOME/FreeSurferColorLUT.txt
for how it works for the aparc+aseg.mgz and the wmparc.mgz. You can embed the LUT in the file itself with
mri_convert file.mgz --ctab yournewLUT file.mgz



On 2/9/2021 5:30 PM, Vinny K wrote:

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Thanks Doug, the commands gave the expected outputs.  I used the original lh and rh BA_exvivo annotations and got the new BA+aseg.mgz and wmBA.mgz files.  Yes, please let me know how to proceed with the new LUT.





On Tue, Feb 9, 2021 at 10:47 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
Look in the subject/scripts/recon-all.cmd file of one of your subjects.
You will find five mri_surf2volseg commands
Use the 2nd one (the one that creates aparc+aseg.mgz) as your template and modify it to take your BA annotation and output a "BA+aseg.mgz"
Use the last one ( the one that creates wmparc.mgz) as your template to create your new wmBA.mgz file, modifying it as needed.
You will need to create a new LUT, but let's do that when you get there

On 2/9/2021 10:26 AM, Vinny K wrote:

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I am using freesurfer-linux-centos7_x86_64-7.1.1-20200723-8b40551

On Tue, Feb 9, 2021 at 9:55 AM Douglas N. Greve <dgreve@mgh.harvard.edu> wrote:
which version of FS are you using?

On 2/5/2021 10:02 PM, Vinny K wrote:

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Hello,

I'd like to obtain white matter parcellations of the Brodmann areas.  I am not certain that the generated wmparc file from recon-all has this type of parcellation.  I was able to convert Brodmann area label files to mgz format using mris_label2annot and mri_aparc2aseg commands.  How can I obtain white matter parcellation of the individual Brodmann area volumes?

Thanks,

Vinny 

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