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Hi Kersten,

Thanks so much for your response. I was actually referred to the qatools-python modulate from someone in my lab in respose to my previous questions. That tool has been working great so far with Freesurfer 6.0 output.

Warm regards, and thanks so much for your help, Kamy

On Jul 13, 2020, at 1:47 PM, Diers, Kersten /DZNE <Kersten.Diers@dzne.demailto:Kersten.Diers@dzne.de> wrote:

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Hello Kamy,

thanks for your mail, and sorry I missed it in last week.

If I understand correctly, you are referring to the QAtools that were originally developed for Freesurfer 5.1 and 5.3, right?

I.e. those at https://surfer.nmr.mgh.harvard.edu/fswiki/QAToolshttps://urldefense.proofpoint.com/v2/url?u=https-3A__surfer.nmr.mgh.harvard.edu_fswiki_QATools&d=DwMGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=KhGiP9W8xiF_0U6IjkXyuA7kQ8FmHzcU4SZVtZYlKyjFb7nhlNPSlsFAXcoNHLMd&m=xnmzi17ibl1It9DLou7L7oMCle1syXLoa7SQbdm3Neg&s=Ju028vEBXqwY9xQAtKh96bHsRkbYcrt-O_qrUVf1yOc&e=

I can run a few test cases tomorrow to confirm, but it may well be that they have issues with Freesurfer 6.0. Not sure if that could be fixed easily, though.

However, that was one reason for us to start developing a revision and extension of the original tools that should work with Freesurfer 6.0, which is the `qatools-python` package that Andrew is referring to. As Andrew writes, its most recent version is available from https://github.com/Deep-MI/qatools-pythonhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Deep-2DMI_qatools-2Dpython&d=DwMGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=KhGiP9W8xiF_0U6IjkXyuA7kQ8FmHzcU4SZVtZYlKyjFb7nhlNPSlsFAXcoNHLMd&m=xnmzi17ibl1It9DLou7L7oMCle1syXLoa7SQbdm3Neg&s=MB094gCiER0Wz31Dh55WzULVoJZST-Dqq9fo5MudFPA&e=. Maybe you can check it out to see if it’s a suitable alternative for you.

Best regards,

Kersten

Am 13.07.2020 um 18:39 schrieb Hoopes, Andrew <AHOOPES@mgh.harvard.edumailto:AHOOPES@mgh.harvard.edu>:

Hi Kamy,

The QA tools are actually developed outside of our lab. It might be helpful to contact the Reuter lab directly - https://github.com/Deep-MI/qatools-pythonhttps://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_Deep-2DMI_qatools-2Dpython&d=DwMGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=KhGiP9W8xiF_0U6IjkXyuA7kQ8FmHzcU4SZVtZYlKyjFb7nhlNPSlsFAXcoNHLMd&m=xnmzi17ibl1It9DLou7L7oMCle1syXLoa7SQbdm3Neg&s=MB094gCiER0Wz31Dh55WzULVoJZST-Dqq9fo5MudFPA&e=

best Andrew

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Wakim, Kathryn-Mary" <KathrynMary_Wakim@urmc.rochester.edumailto:KathrynMary_Wakim@urmc.rochester.edu> Reply-To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Thursday, July 9, 2020 at 7:51 PM To: FS Help <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] QAtools with Freesurfer version 6.0

External Email - Use Caution Hi all,

I’m relatively new to Freesurfer, and I am just beginning to check the output of my recon-alls using QAtools. However, I’m running into a number of difficulties and errors with QAtools, and I’m wondering if this tool is not yet optimized for the current version of Freesurfer.

I have attached the recon_checker.All.summary.log output from QA tools. Below, I’ve also highlighted some of the errors and issues I see in the recon_chcker log file. Please note thatt, per the subject’s recon-all log file, recon-all ran to completion with no errors.

Overview of recon_checker errors:

1) ERROR: Subject 10201003 missing output file ../mri/nu_noneck.mgz

* Note: this is repeated for a number of different output files

2) ERROR: Recon-all steps missing in subject 10201003 status file 3) View your snapshots by opening this file in an internet browser:

* Note: I have attached a screenshot of the output .html file in-browser. Note that I have installed and verified installation of ImageMagick.

Thank you very much for your help, Kamy Wakim

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-- Kersten Diers Image Analysis Group (AG Reuter) German Center for Neurodegenerative Diseases (DZNE) B.1.114 | Building 99 | Venusberg-Campus 1 | 53127 Bonn | Germany https://www.dzne.de/en/sites/bonn/research-groups/reuter.htmlhttps://urldefense.proofpoint.com/v2/url?u=https-3A__www.dzne.de_en_sites_bonn_research-2Dgroups_reuter.html&d=DwMGaQ&c=4sF48jRmVAe_CH-k9mXYXEGfSnM3bY53YSKuLUQRxhA&r=KhGiP9W8xiF_0U6IjkXyuA7kQ8FmHzcU4SZVtZYlKyjFb7nhlNPSlsFAXcoNHLMd&m=xnmzi17ibl1It9DLou7L7oMCle1syXLoa7SQbdm3Neg&s=dw1rjhanlzWRzcwcGtB6Xb5KonuotkJNrcvXh6r93Jw&e= Phone: +49 / 228 / 43302 - 381

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