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Hi,

I have another question. I set ccseg option to get CC stats but they do not show in the final aseg.stats file though it seem that the CC segemntnation is performend ?

Yours Frank ---------------- adj. Prof. Dr. Frank Zoellner Acting head Computer Assisted Clinical Medicine Mannheim Institute for Intelligent Systems in Medicine Medical Faculty Mannheim Heidelberg University Theodor-Kutzer-Ufer 1-3 D-68167 Mannheim

Phone: +49 (0)621 3835117 Fax: +49 (0)621 3835123 Email: Frank.Zoellner@MedMa.Uni-Heidelberg.demailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85PV...

Von: freesurfer-bounces@nmr.mgh.harvard.edu im Auftrag von "Zollei, Lilla,Ph.D." LZOLLEI@MGH.HARVARD.EDU Antworten an: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Datum: Donnerstag, 24. Oktober 2024 um 03:59 An: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs

Dear Frank,

You are correct. The list of segmentation labels is not 100% the same. For the infantFS segmentation labels you can refer to Table 1 in https://secure-web.cisco.com/1yiUa1Vk5ihTnaFGWa_rpomMezNViMShkgspNV0lMBe5DLL...

Best, Lilla ________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Zoellner, Frank Frank.Zoellner@medma.uni-heidelberg.de Sent: Monday, September 23, 2024 4:31 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] infantFS: expected outputs

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Dear Lilla,

Besides the differences in the files, when looking at the segmentations we wondered why there are some labels zero in the aseg stats file.

These are :

Left-Inf-Lat-Vent

CSF

Right-Inf-Lat-Vent

Brain-Stem

Left-vessel

Left-choroid-plexus

Right-vessel

Right-choroid-plexus

5th ventrikel

WM-hypointensities

We also did a cross check and had run the same subject with the normal freesurfer pipeline and here there have been segmentations for the above structures.

Maybe you have an idea what is happening here ? or are these not included in the atlas?

Thanks in advance

Yours

Frank

-----------

adjunct Prof. Dr. Frank Zoellner

Acting head

Computer Assisted Clinical Medicine

Mannheim Institute for Intelligent System in Medicine

Medical Faculty Mannheim

Heidelberg University

Theodor-Kutzer-Ufer 1-3

D-68167 Mannheim

Phone: +49 (0)621 3835121

Fax: +49 (0)621 3835123

Email: Frank.Zoellner@MedMa.Uni-Heidelberg.demailto:Frank.Zoellner@MedMa.Uni-Heidelberg.de

Web: https://secure-web.cisco.com/1m0Kj20FyM86PUSYrf0HbRKDAEbErELxTGijhcN-gjE85PV...

Von: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu Im Auftrag von Zollei, Lilla,Ph.D. Gesendet: Sonntag, 22. September 2024 16:12 An: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] infantFS: expected outputs

Hi Marlene,

This is correct. Even though infant_recon_all is trying to mimic the output folder structure and follows the FreeSrufer naming convention, it does not generate all of the files that the adult version does.

Lilla

________________________________

From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Marlene Staginnus <ms2290@bath.ac.ukmailto:ms2290@bath.ac.uk> Sent: Monday, September 16, 2024 9:57 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] infantFS: expected outputs

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Dear FreeSurfer Team,

Apologies in case I missed this elsewhere, but I was wondering whether there is any information on what the expected outputs of running infant_ recon_all are, similar to this (https://secure-web.cisco.com/1842_5uJLUmhL9zjqueT9IG-O2ijdmDUyVixpX5UWMvoZ6Y...) for the adult pipeline?

I am asking as after testing the pipeline using the example participant provided on openneuro (https://secure-web.cisco.com/1ZFwVrUQPg9OdHj5xfWvCvA6li9k0cO4hetJ6og0O1nRrJY..., I’ve noticed that some of the output differs from the adult version and I wanted to ensure that everything is running correctly before applying it to our data. For example, there is no ‘orig’ subdirectory or orig.mgz file in the ~/mri folder. Similarly, fewer files are included in the ~/stats folder (only: brainvol.stats, lh.aparc.stats, rh.aparc.stats) although I was able to able to generate other files (e.g., aseg.stats) using mri_segstats. Overall, only the following folders are generated following recon-all without errors: label, log, mri, stats, and surf.

Is this correct or might there be something going wrong on my end?

1) FreeSurfer version: infant-dev-4a14499-20210109-4a14499

2) Platform: CentOS release 7

3) uname -a: Linux fhpc-1840 6.8.0-40-generic #40~22.04.3-Ubuntu SMP PREEMPT_DYNAMIC Tue Jul 30 17:30:19 UTC 2 x86_64 x86_64 x86_64 GNU/Linux

4) infant_recon_all log: see attached

Thank you in advance!

Best wishes, Marlene