Mri_normalize: could not open source file /out/freesurfer/sub-110/mri/T2.prenorm.mgz


#1

Hello experts,
I am keep getting following error. I am copying the last paragraph from: recon-all.log. below for your references and I am using docker-in linux. I am wondering if this is due to memory or something else ? If this is a memory related issues, how can i increase the allocated memory to docker ?

commandline function: fmriprep-docker – fs-licence-file /usr/…/.txt data/in/ data/out participant --participitant_level 110 --low-mem

BL
#------------------------------------------------------------------------------------------------------
Applying LTAtransformInterp (resample_type 1)
writing to /out/freesurfer/sub-110/mri/T2.prenorm.mgz…

mri_normalize -sigma 0.5 -nonmax_suppress 0 -min_dist 1 -aseg /out/freesurfer/sub-110/mri/aseg.presurf.mgz -surface /out/freesurfer/sub-110/surf/rh.white identity.nofile -surface /out/freesurfer/sub-110/surf/lh.white identity.nofile /out/freesurfer/sub-110/mri/T2.prenorm.mgz /out/freesurfer/sub-110/mri/T2.norm.mgz

mghRead(/out/freesurfer/sub-110/mri/T2.prenorm.mgz): could not read 409600 bytes at slice 97
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-110/mri/T2.prenorm.mgz…
No such file or directory
(my NOTE: I checked “/out/freesurfer/sub-110/mri/T2.prenorm.mgz” and file exist in this dir)
mri_normalize: could not open source file /out/freesurfer/sub-110/mri/T2.prenorm.mgz
No such file or directory
Linux 71acb67e76f0 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-110 exited with ERRORS at Sat Aug 4 21:43:35 UTC 2018

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


#2

Isn’t this a duplicate of Could not read error : while file “:/out/freesurfer/sub-001/mri/T2.prenorm.mgz” exist?