Try something like this

mris_anatomical_stats -th3 -mgz -cortex ../label/lh.cortex.label -f ../stats/lh.lobe.stats -b -a ../label/lh.lobe.annot fsm010 lh white

On 9/8/2020 7:58 AM, Marina Fernández wrote:

External Email - Use Caution

Dear experts,

I would like to get a .stats file this the volume and thickness of lobe annotation, so I am following the steps indicated in this link https://surfer.nmr.mgh.harvard.edu/fswiki/CorticalParcellation. Specifically, I used these commands:

mri_annotation2label --subject s_001 --hemi lh --lobesStrict lobe.annot cd /usr/local/freesurfer/subjects/; mris_anatomical_stats -a s_001/label/lh.lobe.annot -f s_001/stats/lh.lobe.stats -b s_001 lh

The output file that I get (lh.lobe.stats) seems normal and contains the measurements that I need (volume and thickness). The problem is that the terminal output contains this error message: ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot (below you can find the full terminal output)

What I have to do to obtain the lh.lobe.stats file (with the same or similar stucture) without the error message?

Best regards, Marina

% /TERMINAL OUTPUT / % /

subject = s_001 annotation = aparc hemi = rh surface   = white

Reading surface  /usr/local/freesurfer/subjects/s_001/surf/rh.white Loading annotations from /usr/local/freesurfer/subjects/s_001/label/rh.aparc.annot reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) Seg base 2000 MRISmergeAnnotations: parcCount=11, newparcname=frontal mri_annotation2 supposed to be reproducible but seed not set MRISmergeAnnotations: parcCount=9, newparcname=temporal MRISmergeAnnotations: parcCount=5, newparcname=parietal MRISmergeAnnotations: parcCount=4, newparcname=occipital MRISmergeAnnotations: parcCount=4, newparcname=cingulate computing statistics for each annotation in s_001/label/rh.lobe.annot. reading volume /usr/local/freesurfer/subjects/s_001/mri/wm.mgz... reading input surface /usr/local/freesurfer/subjects/s_001/surf/rh.white... Using TH3 vertex volume calc Total face volume 176610 Total vertex volume 173305 (mask=0) reading input pial surface /usr/local/freesurfer/subjects/s_001/surf/rh.pial... reading input white surface /usr/local/freesurfer/subjects/s_001/surf/rh.white... reading colortable from annotation file... colortable with 8 entries read (originally none)

table columns are:     number of vertices     total surface area (mm^2)     total gray matter volume (mm^3)     average cortical thickness +- standard deviation (mm)     integrated rectified mean curvature     integrated rectified Gaussian curvature     folding index     intrinsic curvature index     structure name

ERROR: stating file /usr/local/freesurfer/subjects/s_001/label/s_001/label/rh.lobe.annot atlas_icv (eTIV) = 1198953 mm^3    (det: 1.624839 ) 37262  24668  63218  2.363 0.474     0.124     0.029  414    43.8  frontal  3602   2412   6370  2.374 0.615     0.137     0.027 54     3.8  cingulate 12917   8443  18251  2.024 0.428     0.134     0.030  171    15.6  occipital 19235  12890  36112  2.488 0.535     0.119     0.028  211    21.0  temporal 26568  17417  41499  2.204 0.466     0.119     0.024  287    25.6  parietal  2510   1617   4741  3.018 0.820     0.126     0.036 28     3.9  insula/

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