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
<dgr...@mgh.harvard.edu <mailto:dgr...@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:
External Email - Use Caution
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
<dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote:
which version of FS are you using?
On 2/5/2021 10:02 PM, Vinny K wrote:
External Email - Use Caution
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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