Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats

[Fischl, Bruce]

Glad to hear it
Bruce

From: freesurfer-boun...@nmr.mgh.harvard.edu 
<freesurfer-boun...@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


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Hi Bruce,

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

Best,
Luqi
On 4/13/2022 21:46，Fischl, 
Bruce<bfis...@mgh.harvard.edu><mailto:bfis...@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-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 11:22 PM
To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Wrong thickness values with mris_anatomical_stats


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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


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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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