External Email - Use Caution
Got it. Thank you very much for your replies and attention, Bruce! It
helped me a lot.
Em dom., 10 de set. de 2023 às 17:07, Fischl, Bruce R.,PHD <
bfis...@mgh.harvard.edu> escreveu:
> External Email - Use Caution
>
> Yes, although they would be generated in the same way across subjects with
> either method
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Leonardo Cardoso
> Saraiva
> *Sent:* Sunday, September 10, 2023 4:07 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between
> resampled and recon-all generated annot files
>
>
>
> * External Email - Use Caution *
>
> Thank you once more for your response, Bruce!
>
> I intend to only use the parcellations that were initially mapped onto
> fsaverage and subsequently resampled to the subjects' native surfaces. This
> should ensure that the parcellations for all subjects are generated in the
> same way, right?
>
> Many thanks again!
>
> Best,
> Leo
>
>
>
> Em dom., 10 de set. de 2023 às 15:55, Fischl, Bruce R.,PHD <
> bfis...@mgh.harvard.edu> escreveu:
>
> * External Email - Use Caution *
>
> Yes, although I expect the individual subject parcellations to be a bit
> more accurate than the ones mapped from fsaverage. Probably not enough to
> make a significant difference though
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Leonardo Cardoso
> Saraiva
> *Sent:* Sunday, September 10, 2023 3:53 PM
> *To:* Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
> *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between
> resampled and recon-all generated annot files
>
>
>
> * External Email - Use Caution *
>
> Many thanks for reaching out and providing such clear information, Douglas
> and Bruce! I really appreciate it.
>
> I was indeed comparing the ?h.aparc.annot files produced by recon-all to
> those produced by mri_surf2surf.
>
> The aim of my analyses is to compare groups in morphometric features,
> using parcellations initially generated in fsaverage and then resampled to
> each subject's native surface. Based on the information you provided, it
> sounds like my approach is valid as long as I consistently use the
> mri_surf2surf command with identical arguments for all subjects within each
> group. Is that correct?
>
> Thanks again for your time and attention!
>
> Best,
> Leo
>
>
>
> Em dom., 10 de set. de 2023 às 14:19, Fischl, Bruce R.,PHD <
> bfis...@mgh.harvard.edu> escreveu:
>
> * External Email - Use Caution *
>
> Actually there is a whole Bayesian segmentation on the surface procedure
> that generates the individual subject parcellation so it definitely won’t
> be the same as just mapping fsaverage
>
>
>
> Cheers
>
> Bruce
>
>
>
> *From:* freesurfer-boun...@nmr.mgh.harvard.edu <
> freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *Douglas N. Greve
> *Sent:* Sunday, September 10, 2023 1:35 PM
> *To:* freesurfer@nmr.mgh.harvard.edu
> *Subject:* Re: [Freesurfer] Discrepancy in vertex counts between
> resampled and recon-all generated annot files
>
>
>
> * External Email - Use Caution *
>
> Which annot files are you comparing? Some of them (eg, aparc) have an
> extra procedure where the labels boundaries are fine-tuned, so that could
> cause the difference. Your command looks right.
>
> On 8/30/2023 1:28 PM, Leonardo Cardoso Saraiva wrote:
>
> * External Email - Use Caution *
>
> Dear Freesurfer Experts,
>
> I would like to follow up on my last email and ask if you had a chance to
> take a look at it.
>
> Any guidance or feedback would be greatly appreciated!
>
> Thank you for your time!
>
> Best,
> Leo
>
>
>
> Em dom., 20 de ago. de 2023 às 23:41, Leonardo Cardoso Saraiva <
> leonardo.sara...@usp.br> escreveu:
>
> Dear Freesurfer Experts,
>
> I am using .annot files to extract parcellated vertex-wise morphometric
> features from surf files (e.g., area value from ?h.area file). For each
> vertex, I want to determine the parcel it belongs to and its associated
> morphometric features. During this process, I exclude vertices labeled as
> ‘unknown’ or ‘medial wall’.
>
> In addition to the aparc parcellation, I am also using other parcellations
> computed on fsaverage. Therefore, I need to resample these parcellations
> onto native surfaces. To do this, I am using commands such as the one
> below:
>
>
>
> mri_surf2surf --srcsubject fsaverage \
> --sval-annot ${SUBJECTS_DIR}/fsaverage/label/lh.test\
> --trgsubject sub-test \
> --trgsurfval ${SUBJECTS_DIR}/sub-test/label/lh.test \
> --hemi lh
>
>
>
> As a sanity check, I used the above command to resample the aparc
> parcellation onto native surfaces (which is already done by recon-all).
> However, when I use the .annot files generated by the above command to
> extract morphometric features from surf files, I get a different number of
> vertices than when I use the .annot files generated by recon-all. Is this
> behavior expected? Am I doing something wrong?
>
> Thank you for your time and attention.
>
> Best,
>
> Leo
>
>
>
>
>
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