I think you mean “th3” not “thr3”. It is interpreting it as an option to use a
different thickness file (specified by the next thing on the command line,
which is “-mgz”.
Cheers
Bruce
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats
External Email - Use Caution
Hi Yulin and Bruce,
Thanks for your quick replies. I tested FS v6.0 and v7.2 with the following
command, and got the same results.
mris_anatomical_stats -thr3 -mgz -f ./lh.aparc.stats -b -a
$SUBJECTS_DIR/100307/label/lh.aparc.annot 100307 lh white
using thickness file -mgz.
computing statistics for each annotation in
/dat03/data/HCP1200_FS//100307/label/lh.aparc.annot.
reading volume /dat03/data/HCP1200_FS//100307/mri/wm.mgz...
reading input surface /dat03/data/HCP1200_FS//100307/surf/lh.white...
Using TH3 vertex volume calc
Total face volume 245583
Total vertex volume 241389 (mask=0)
reading input pial surface /dat03/data/HCP1200_FS//100307/surf/lh.pial...
reading input white surface /dat03/data/HCP1200_FS//100307/surf/lh.white...
error: No such file or directory
error: MRISreadCurvature: could not open
/dat03/data/HCP1200_FS//100307/surf/lh.-mgz
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
atlas_icv (eTIV) = 1512540 mm^3 (det: 1.287970 )
1297 908 2459 0.000 0.000 0.096 0.015 9 0.9 bankssts
928 588 1875 0.000 0.000 0.130 0.025 12 1.0 caudalanteriorcingulate
3498 2347 6757 0.000 0.000 0.116 0.024 32 3.7 caudalmiddlefrontal
2196 1350 2877 0.000 0.000 0.145 0.036 34 3.6 cuneus
657 427 1942 0.000 0.000 0.135 0.047 9 1.5 entorhinal
Best,
Luqi
On 4/12/2022 21:41，Huang,
Yujing<yhuan...@mgh.harvard.edu><mailto:yhuan...@mgh.harvard.edu> wrote：
Hi Luqi,
I’m wondering how you ran mris_anatomical_stats. Can you send the command?
I noticed 2 things in the error output:
1. The filename has a ‘-‘ after the ‘.’
2. lh files should not have ‘mgz’ extension
Best,
Yujing
From:
freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>>
On Behalf Of lqcheng2017
Sent: Tuesday, April 12, 2022 9:09 AM
To: freesurfer
<freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>>
Subject: [Freesurfer] Wrong thickness values with mris_anatomical_stats
External Email - Use Caution
Dear experts,
I thied to calculate measures using mris_anatomical_stats. All the measures
seems right excepted that the thickness is 0. I noticed a error as follows:
MRISreadCurvature: could not open /dat02/subjects/sub001/surf/lh.-mgz
No such file or directory
Could you have any ideas to solve the problem?
Thank you very much.
Best,
Luqi
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