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 <fischl@nmr.mgh.harvard.edumailto:fischl@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

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer