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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Marlene Staginnus
<ms2...@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 (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 (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
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