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Hi Kersten,

Ah yes, that would be it. I am using data from a 7T scanner, so wanted it to be processed at the best resolution possible, hence using the -cm command.

Many 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: Tuesday, 17 October 2023 at 12:12 am
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] [WARNING: ATTACHMENT(S) MAY CONTAIN MALWARE]Re: Stools error query

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Hello Elizabeth,

thank you for giving the new version of the toolbox a try as well.

Since the error persists: my suspicion is that not all of your images have the canonical ("FreeSurfer - conformed") dimensions of 256 x 256 x 256 voxels, maybe because they were processed with FreeSurfer's high-resolution processing variant / the recon-all ... -cm ... command?

If that's indeed the case, I will try to update the toolbox to be able to deal with images that have dimensions different from 256 x 256 x 256.

Best regards,

Kersten

On Sun, 2023-10-15 at 23:37 +0000, Elizabeth Haris wrote:

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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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