Could not read error : while file ":/out/freesurfer/sub-001/mri/T2.prenorm.mgz" exist


#1

Hello,
Received following error almost at the end of the pipeline.
Any idea why this could be ?

Thanks
BL

Applying LTAtransformInterp (resample_type 1)
writing to /out/freesurfer/sub-001/mri/T2.prenorm.mgz…

mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /out/freesurfer/sub-001/mri/aseg.presurf.mgz -surface /out/freesurfer/sub-001/surf/rh.white identity.nofile -surface /out/freesurfer/sub-001/surf/lh.white identity.nofile /out/freesurfer/sub-001/mri/T2.prenorm.mgz /out/freesurfer/sub-001/mri/T2.norm.mgz

mghRead(/out/freesurfer/sub-001/mri/T2.prenorm.mgz): could not read 409600 bytes at slice 231
using Gaussian smoothing of bias field, sigma=0.500
disabling nonmaximum suppression
retaining points that are at least 1.000mm from the boundary
using segmentation for initial intensity normalization
reading from /out/freesurfer/sub-001/mri/T2.prenorm.mgz…
No such file or directory
mri_normalize: could not open source file /out/freesurfer/sub-001/mri/T2.prenorm.mgz
No such file or directory
Linux f3b30f91ee80 3.16.0-30-generic #40~14.04.1-Ubuntu SMP Thu Jan 15 17:43:14 UTC 2015 x86_64 x86_64 x86_64 GNU/Linux

recon-all -s sub-001 exited with ERRORS at Tue Jun 5 19:09:49 UTC 2018

To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting


#2

You need to provide a few more details:

  • Was it FMRIPREP that you run?
  • Which version?
  • What commandline did you run?
  • Were you reusing precomputed freesurfer outputs?
  • Are you using Docker or Singularity?

#3

Hi Chris,
I had to kill preprocessing at the middle, and re-ran without deleting precomputed files. But , it went well after cleaning the precomputed files/folder-no more errors.
(using Docker, version: V1.0.15). Thanks