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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,