That basically looks right. One thing to note  is that you are sampling onto the average surface (fsaverage); this is not really doing surface-based analysis, it will be about the same as registering you individual subject to the mni152, then sampling your ROI atlas onto the individual subject's brain. There are not crucial diffs between fsaverage and mni152, just some small registration diffs that will be accounted for with the --mni152reg flag. I'm not sure what you mean by how to get a volume or surface file from the annot.

On 1/18/2023 2:55 PM, Beatriz Cavendish wrote:

External Email - Use Caution

Hello FreeSurfer Community!

I previously asked a question about volume quantification using an external atlas (in fact, there are 20 brain masks corresponding to the regions of interest). I managed to perform the quantification with the following commands and would like to know if everything is correct:

Use mri_vol2vol to upsample to 1mm:

/usr/local/freesurfer/subjects# mri_vol2vol --mov '/home/pedro/Downloads/Sallet_ROIs/Cluster1_L.nii'  --targ '/usr/local/fsl/data/standard/MNI152_T1_1mm_brain.nii.gz' --regheader --o Cluster1_L_1mm.nii --interp nearest

Use mri_vol2surf to create surface in XXX space:

/usr/local/freesurfer/subjects# mri_vol2surf --mov Cluster1_L_1mm.nii --mni152reg --hemi lh --surf white --o lh.ROIA.mgh

Visualize surface:

/usr/local/freesurfer/subjects# freeview -f $FREESURFER_HOME/subjects/fsaverage/surf/lh.inflated:overlay='/usr/local/freesurfer/subjects/lh.ROIA.mgh'

Convert surface to annotation file:

/usr/local/freesurfer/subjects# mris_seg2annot --seg lh.ROIA.mgh --s fsaverage --h lh --ctab-auto --o lh.ROIA.annot

  Project the atlas to the subject's brain
  <https://secure-web.cisco.com/1JEN07txiABM5huyz9SEUPTihLYxW1TkkC2uDoF7TiUhSsgP-OVVFI-GhV_NS0ilirjStiVAsoXZqTu_h-o5KgPixXxokZUbw6bR3v_907Q6fsQ0Fklts0ATLNGjUiteJLUrycfBI16zuq5m7FTxz4ZlP8PCtdlzdriyhq-G2O728SnNqed2iIo7aNASkfX-HysAZqSHdJf5HMhwqh2M18xbxdW7pBqZvzhxZYqUB7uaVD2iTyDpP2_3T9nkVMRvOTp7dKOT9UtaSGMN2A91YhwHvSEc4jnBSkyDXHoy1v7Npsiu97fIfAQ0RKdrxwOuaD9YRk4EEX-Y2JeTAiPKV1w/https%3A%2F%2Fbhvieira.github.io%2Fblog%2F2022%2F07%2FFreesurferGetStatsNewAtlas%2F%23step_3_project_the_atlas_to_the_subjects_brain>:

/usr/local/freesurfer/subjects# mri_surf2surf --srcsubject fsaverage --trgsubject bert --hemi lh --sval-annot fsaverage/label/lh.ROIA.annot --tval bert/label/lh.bert.ROIA.annot

  Calculate the atlas statistics
  <https://secure-web.cisco.com/1qVy6szcbmCutI-Y6GHK6daTo060hOEJXywT8OVArAV-2IKYUs6mWBEvP4qVojjzMlxZECEKUvXYV1XY7CzsHfH9eIDNvI3qaqw_MX06pgKizqOynSWMPNPHMV_mC_VC82GxM_hYOCzKfdLQdcMyFB7i0fOg1CbSPcCjUx1pL-cCQETIUhGZrPm_km2u2F_mLTsTa4DE8BXXyblZ3KgsDZMIY1Jc7h6QnaRUkVaJmF3IrYyLubqIN8RtGJe1Jmk58uvmXiXnl3IQrX4iMCS0n_qm4rsguiSgVwWmdTDr9bRvnfAnrDPgtXQOgxEjvGyp2m0Ip6ZTVajk1zWnjIOvBMw/https%3A%2F%2Fbhvieira.github.io%2Fblog%2F2022%2F07%2FFreesurferGetStatsNewAtlas%2F%23step_4_calculate_the_atlas_statistics>:

/usr/local/freesurfer/subjects# mris_anatomical_stats -th3 -mgz -cortex $SUBJECTS_DIR/bert/label/lh.cortex.label -f $SUBJECTS_DIR/bert/stats/lh.ROIA.stats -b -a $SUBJECTS_DIR/bert/label/lh.bert.ROIA.annot bert lh white

Some questions:

The projection of the mask volume in the MNI152 space onto the fsaverage space is fully matched. Are there any crucial differences between these spaces?

How to get volume or surface file from annot file?

Best regards,

-- Beatriz Araújo Cavendish, MSc

PhD student | Psychologist

University of São Paulo

São Paulo/SP - Brazil

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