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