Hi Mehul,

Mehul Sampat wrote:

Thanks Doug.

Using mri_label2vol is a good idea and I will use this approach. Now to create the individual binary masks I just need to use mri_label2vol, followed by mri_binarize:

For example:

a. mri_label2vol --seg aparc+aseg.mgz --regheader rawavg.mgz --o aparc+aseg-in-rawavg.mgz --temp aparc+aseg.mgz

The template here should be rawavg.mgz, I think.

b. mri_binarize --i aparc+aseg-in-rawavg.mgz --match 1022 --o lh-postcentral.nii

Also, when I looked at the help, I first thought I could do the same thing with mri_annotation2label followed by mri_label2vol .

for example:

a. mri_annotation2label --subject bert --hemi lh --annotation aparc --outdir labels b. mri_label2vol --label ../labels/lh.postcentral.label --regheader rawavg.mgz --o lh-postcentral.nii --temp aparc+aseg.mgz

Again, use rawavg.mgz as the temp. Also you should be able to use mri_label2vol directly on the annotation (with --annot).

doug

But when I checks the results, (from using mri_annotation2label followed by mri_label2vol), the individual binary mask looks incorrect Did I make an error in the second approach ?

Thanks Mehul

On Tue, Jul 13, 2010 at 2:41 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:

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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