Hello,
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.
I received the following errors with each command, respectively:
mri_anatomical_stats:
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)
(And the table column of “average cortical thickness” (in my case, T1w/T2w ratio) are all 0.000s for the 7 Yeo Networks)
mri_segstats:
Command: 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
output + error: 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
I am running macOS Monterery 12.4, Freesurfer 6.0.0.
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.
Best, Austin
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