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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@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, YujingYHUANG43@mgh.harvard.edumailto:YHUANG43@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of lqcheng2017 Sent: Tuesday, April 12, 2022 9:09 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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

Glad to hear it Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of lqcheng2017 Sent: Thursday, April 14, 2022 2:40 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats

External Email - Use Caution Hi Bruce,

It worked when I changed "thr3" to "th3". Thanks again.

Best, Luqi On 4/13/2022 21:46，Fischl, BruceBFISCHL@mgh.harvard.edumailto:BFISCHL@mgh.harvard.edu wrote： 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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of lqcheng2017 Sent: Tuesday, April 12, 2022 11:22 PM To: freesurfer@nmr.mgh.harvard.edumailto: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, YujingYHUANG43@mgh.harvard.edumailto:YHUANG43@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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of lqcheng2017 Sent: Tuesday, April 12, 2022 9:09 AM To: freesurfer <freesurfer@nmr.mgh.harvard.edumailto: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