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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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External Email - Use Caution 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
External Email - Use Caution 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://secure-web.cisco.com/1vihlX2KA8EhTyjW8rX-kM6b47RY7Wa93rmiqAPD3aJRtvH...https://secure-web.cisco.com/1qVzbBOmbAq6CLsJURwFbYk1OnFTRlQmC3pOCUNhTJ-te1GfvL_15kWPyF0fH9XyN5BD7JT9r_ZvrY3V1uN7QAiFk9lTPE_avB3PIiO3Zevib0gCZlgU20LkuCEa7iP8KTq-Y6sbC8w_mTWW7ZeSFvFDDlCQY2jYf2k0d26bFb6dIDYblSdOMBHkc08XABRWShkn0fjvrxZY4uD94o-3_yB9Q53QYZknaab1tIKR7l1Z2UHZmc273nvQJ7bp71UPLVMA5DjhC1AHBvnjPqE2PQnP4mNi2bRwlitsdKXQvYjSyGY95OiPj_G864gDlc1-V04txwADGIOAV6KsdzJDg5A/https%3A%2F%2Fgithub.com%2FDeep-MI%2Ffsqc?
Thanks,
Kersten
On Thu, 2023-10-12 at 00:23 +0000, Elizabeth Haris wrote: CAUTION: This email originated from outside of DZNE. Do not click links or open attachments unless you recognize the sender and know the content is safe. ACHTUNG: Dies ist eine externe E-Mail, bitte seien Sie vorsichtig beim Anklicken von Links oder Öffnen von Anhängen
External Email - Use Caution 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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