I have created surfaces that contain T1w/T2w ratios (see Glasser & van Essen, 2011; Ganzetti et al., 2014 for details). I am looking to extract the average T1w/T2w value for each of the 7 Yeo networks from the surfaces. We wish to extract intensities from the surface to avoid partial voluming effects that we have observed when extracting whole-brain T1w/T2w values from the T1w/T2w ratio maps (volumes) using a cortical gray matter mask. I have previously tried using mri_anatomical_stats and mri_segstats to do this without success.

command:

mris_anatomical_stats -t lh_<T1w/T2w_ratio_surface>.mgh -a <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot -b subject lh

output + error:

using thickness file lh_<T1w/T2w_ratio_surface>.mgh.

computing statistics for each annotation in <freesurfer_path>/lh.Yeo2011_7Networks_N1000.annot.

reading volume /subject/mri/wm.mgz...

reading input surface /subject/surf/lh.white...

Using TH3 vertex volume calc

Total face volume 306338

Total vertex volume 302976 (mask=0)

reading input pial surface /subject//urf/lh.pial...

reading input white surface /subject/surf/lh.white...

ERROR: number of vertices in lh_<T1w/T2w_ratio_surface>.mgh does not match surface (163842,154532)

mri_segstats --i lh_MM_cbpd_brannon_age_gender_n157_glm_fwhm_src5trg5.mgh --seg ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot --avgwf test.dat

Loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot

mri_read(): couldn't determine type of file ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot

ERROR: loading ../../../../../freesurfer/fsaverage/label/lh.Yeo2011_7Networks_N1000.annot

Can anyone please advise if I am using mri_anatomical_stats or mri_segstats incorrectly, or if there is a better way to extract average T1w/T2w values from the surface directly? Thank you in advance for any help.