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This is probably just an issue near the border. mri_label2label will map each label separately, so there are vertices on the edge that will have multiple labels. I don't think this is a problem as it will be pretty minor. Note that you can also map the annotation itself instead of the individual labels. The same problem exists, and you'll probably get close to the same thing, but you won't get those warnings and it will be simpler. Try something like mris_apply_reg --sval-annot lh.your.annot --streg fsaverage/surf/lh.sphere.reg subject/surf/lh.sphere.reg --tval subject/label/lh.yourannot

On 5/9/2023 7:31 PM, Nadvar, Negin wrote:

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Good afternoon,

Absolutely. Here’s the explanation of the issue in more detail. I have already recon-all’d a subject’s T1W image. Now, I’m trying to use the HCP atlas annotation files in fsaverage space (downloaded from here https://secure-web.cisco.com/1RUlbihl_P7o4iECkLXdYd7_A71_OWggWGKTcu9o3hEd1Q-TIbJydYcpaMQ6fo6JrKecYvuag9pRj0svtM-tbZHyzOf--ziIZbRt3KZ-s273-wWXgwuWLz3_j6DIrKSiJB9xDfjO7TXoRlBY6j7PD0gZvue_aciq07dI505bqMEmXZ1uP3F-_aCwFXl914_RjYxLmyD2BW3AIYseqx3VO4-lgJJvB1qOkeqtl9XALsZFZTVmYtg3Zjfia6F0tH82nhvFtLOak0mCYm9rH0ZcvOg/https%3A%2F%2Ffigshare.com%2Farticles%2Fdataset%2FHCP-MMP1_0_projected_on_fsaverage%2F3498446) to ultimately make the individual ROIs defined in this atlas in the subject-specific volumetric space. In order to do that, I used “mri_annotation2label” to find the label files related to the HCP atlas in the fsaverage space and then I used “mri_label2label” to transform each label to subject-specific space. Then, I used mris_label2annot to create the annotation file in subject-specific space and from there I used mri_aparc2aseg to create a volumetric .nii file in which each ROI is labeled with a different number. From here I was able to extract each ROI in the subject-specific space.

Even though I was able to create my ROIs of interest at the end, I noticed that during the execution of the “mris_label2annot” I got warnings stating that some vertices mapped to multiple labels. This indicates that during the conversion in the prior step using “mri_label2label”, some vertices were assigned to multiple labels, however, I’m not sure how I could have prevented this from happening. Here’s the syntax I used for the left hemisphere as an example:

mri_label2label --srcsubject fsaverage --srclabel XYZ1 --trgsubject XYZ2 --trglabel XYZ3 --regmethod surface --hemi lh

Please let me know if I should have included a certain flag while executing “mri_label2label” that could have avoided the label overlaps in the new space.

Thank you,

Negin

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*From:* freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@mgh.harvard.edu *Sent:* Monday, May 8, 2023 10:47 AM *To:* freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] Question about volumetric atlas ROIs overlap

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I don't understand what you are referring to. Can you elaborate?

On 5/5/2023 7:53 PM, Nadvar, Negin wrote:

...

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Hello,

I have a general question about handing atlas ROIs after applying recon-all on a T1W image. Could you please clarify how I can minimize/prevent atlas ROIs overlap in volumetric subject-specific space when going from surface-based space to volumetric space?

Please let me know if you need more information.

Thanks in advance, Negin

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