I think either should work, though I am more comfortable with mri_vol2vol. Depending on what you are doing you might want to use mri_label2vol. This can convert the aseg.mgz directly to the native anatomical space. The main difference is that it will resolve boundary voxels by voting. With your method, you will have some voxels that will be in more than one label, which may or may not be a problem depending on what you are doing.
doug
Mehul Sampat wrote:
Hi Folks,
I would like to create binary masks for any given structure in aseg.mgz and aparc+aseg.mgz. I would then also like to map the masks back to native space.
I think, I should use mri_binarize followed by mri_convert as shown in the two examples below:
Example 1: a. mri_binarize --i mri/aseg.mgz --match 10 --o deep-gm-rois/lh-thalamus.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii
Example 2: a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o ctx-gm-rois/lh-postcentral.mgz b. mri_convert -rl mri/orig/001.mgz -rt nearest ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii
Ques 1: Is the best approach for this task ?
I noticed in the FAQ that mri_vol2vol is recommended for conversion from freesurfer space to anantomical space.
Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice option ? Thanks Mehul
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