External Email - Use Caution
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
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
MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://pmc.ncbi.nlm.nih.gov/articles/PMC7415702/.
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
External Email - Use Caution
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
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.edu
<freesurfer-bounces@nmr.mgh.harvard.edu>
on behalf of Marlene Staginnus <ms2290@bath.ac.uk>
Sent: Monday, September 16, 2024 9:57 AM
To: freesurfer@nmr.mgh.harvard.edu
<freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] infantFS: expected outputs
External Email - Use Caution
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 (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllOutputFiles)
for the adult pipeline?
I am asking as after testing the pipeline using the example participant provided on openneuro (MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://openneuro.org/datasets/ds004776/versions/1.0.0,
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