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