I am willing to compute the volume of a given structure, say the right caudate. This structure has the index number 50 (as per desc-aseg_dseg.tsv, and consistently with freesurfer stats file).
From freesurfer stats for my subject, I get a volume (in mm3) of 3410.8 (for a NVoxels of 3438).
So my guess is that this volume should match the one of the voxels with value == 50 in sub-01_desc-aseg_dseg.nii.gz. When I count the number of voxels, I get 3726. This is not the same as in freesurfer, but this is also not (yet) a contradiction because voxel size might differ.
To get the volume, I extract the voxel size (using nibabel header.pixdim[1:4] and multiplying the entries).
This yields a voxel size of 0.99208842. The volume, from fmriprep outputs, is then
So there is a mismatch in volumes: from freesurfer output (generated by fmriprep, saved in fmriprep/sourcedata/freesurfer) I get 3410.8mm3 while from directly computing from the aseg.dseg.nii.gz image I get 3274.8046875 mm3.
This difference is not small, so there is something to understand…