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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
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@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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