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Hi Kersten,

 

I ran the fsqc, but am still getting the same error for 45 of my 72 participants (outlined below). I’ve attached the logfile and the csv output if that helps.

 

Starting fsqc for subject 630 at 2023-10-16 10:09 AEDT

Computing white and gray matter SNR for orig.mgz ...

ERROR: SNR computation failed for 630

Reason: index 256 is out of bounds for axis 2 with size 256

Computing white and gray matter SNR for norm.mgz ...

ERROR: SNR computation failed for 630

Reason: index 256 is out of bounds for axis 2 with size 256

 

Thanks,

Elizabeth

 

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Diers, Kersten /DZNE <Kersten.Diers@dzne.de>
Date: Thursday, 12 October 2023 at 10:06 pm
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Stools error query

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Hi Elizabeth,

 

the qatools / fsqc tools have evolved quite a bit since their inclusion in FS 7.1.

 

Would it be possible for you to try their newest version, available from MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://github.com/Deep-MI/fsqc?

 

Thanks,

 

Kersten

 

On Thu, 2023-10-12 at 00:23 +0000, Elizabeth Haris wrote:

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Hi there,

 

I am running into a problem when using qatools.py to qa my recon-all. Some of my participants process ok, but with others I get the error below. Any advice on what to do to address this?

 

Many thanks,

Elizabeth

 

ERROR:

 

Computing white and gray matter SNR for orig.mgz ...

Traceback (most recent call last):

 File "/Applications/freesurfer_v7.1.0/python/scripts/qatools.py", line 17, in <module>

   qatoolspython.run_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table)

 File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 883, in run_qatools

   _do_qatools(subjects_dir, output_dir, subjects, shape, screenshots, fornix, outlier, outlier_table)

 File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/qatoolspython.py", line 663, in _do_qatools

   wm_snr_orig, gm_snr_orig = checkSNR(subjects_dir, subject, SNR_AMOUT_EROSION, ref_image="orig.mgz")

 File "/Applications/freesurfer_v7.1.0/python/packages/qatoolspython/checkSNR.py", line 83, in checkSNR

   b_wm_data[x,y,z] = 1

IndexError: index 256 is out of bounds for axis 2 with size 256

 

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