Use mri_binarize --match segid --i aseg.mgz --o mask.mgz
where segid is the segmentation code (eg, left hippo is 17) from
$FREESURFER_HOME/FreeSurferColorLUT.txt
On 7/21/2019 2:09 AM, Dandil dNd wrote:
External Email - Use Caution
Hi Bruce,
Thank you for your reply. I want to create a 3D matrix (based on the aseg.mgz
and the lookup table) in which the elements of a specific region will be 1 and
the other regions will be 0. I can do this via Matlab, but since I should do
some format transformations, I am not sure if the orientation or other
parameters remains intact. So I want to choose a more reliable solution.
Best Regards,
Dandil
On Sat, Jul 20, 2019 at 8:06 PM Bruce Fischl
<fis...@nmr.mgh.harvard.edu<mailto:fis...@nmr.mgh.harvard.edu>> wrote:
Hi DnD
what kind of region masks do you mean? You can probably use
mri_binarize -match ...
mri_mask
to do what you want. Not sure what zero_ltgt_4dfp, but it is not ours
cheers
Bruce
On
Sat, 20 Jul 2019, Dandil dNd wrote:
>
> External Email - Use Caution
>
> Hi dear FS users,
>
> I have performed recon-all on my dataset, and now I want to create region
> masks using the lookup table. I have found the command "zero_ltgt_4dfp" to
> do this, but this error comes up: "zero_ltgt_4dfp: command not found".
> Can anyone kindly help me to solve the problem?
>
> Best Regards,
> DnD
>
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