So you want to map the labels in fsaverage into MNI152 volumes pace, right? After mris_divide_parcellation, you should have a parcellation in fsaverage space. Use mri_surf2surf (or mris_apply_reg) to map that into the MNI152 that you ran recon-all on. Look in the recon-all.log file for the command that created the aparc+aseg.mgz file (mri_aparc2aseg). Change that command line to use your new annotation, and specify a different output. If you want to view it in freeview, then you will also need to create a new color table like $FREESURFER/FreeSurferColorLUT.txt but it will need your new labels in it. You can get the indicies by loading the volume into freeview and clicking on the labels.

On 11/3/2021 4:41 AM, Alvarado,Luis R wrote:

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Hi all,

I am having a bit of a hard time figuring out the best option to convert surface labels to mni volume masks.

For my ROI FS analysis, I divided the fsaverage S1 and M1 labels into 5 sub-labels using *mris_divide_parcellation*. I then used *mri_label2label* to map those labels to each of my subjects to study differences in thickness among 2 groups.

I am now trying to map those same labels from fsaverage to mni space in order to use them as ROI for resting-state connectivity analysis in the conn toolbox pipeline. From reading The Mail Archive I have come across multiple pieces of advice on how one might go about doing this. These range from a) using *mri_label2vol* and *mri_vol2vol*; b) creating a new annotation file for fsaverage from the labels and using *mri_aparc2aseg* and then *mri_vol2vol*; to c) running mni152 through *recon-all*.

As you can probably tell by now, I am a bit confused about the most efficient and accurate way to accomplish this.

any advice would be greatly appreciated.

Luis R. Alvarado

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