fMRIprep: ?h.white.K files missing after freesurfer preprocessing

#1

Hi! I’m trying to run freesurfer analysis on stuctural data preprocessed through fmriprep. However, when I try to run the -qcache flag, I get an error that /$SUBJECTS_DIR/subject/surf/?h.white.K file is missing and so recon-all exits with an error. This file is missing for all subjects, and none of the freesurfer logs show any error at exit. Any ideas about where this file went? Thanks in advance!

#2

Could this be the problem - https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg57231.html? Can you attach FreeSurfer’s log file?

#3

Hi @oesteban, that does seem to be the same problem. I’ve run other datasets through freesurfer without fmriprep and never encountered it, so I was wondering if it was fmriprep-specific. I’m attaching one of the log files for freesurfer here. Thanks!
recon-all.txt (427.8 KB)

#4

Hi @megha,

$ tail -n1 recon-all.txt 
recon-all -s sub-030 finished without error at Thu Mar  7 11:40:36 UTC 2019

Does this log file belong to a different run?

#5

No… I only ran recon-all on these subjects once. Do you want me to send the log file for when the -qcache flag failed?