Dear Courtney,
You can safely ignore “This file does not contain MRI parameters”. If the output files are not created, there must be another error further down. Could you please send us the whole output?
Cheers,
/Eugenio
Juan Eugenio Iglesias
Senior research fellow
CMIC (UCL), MGH (HMS) and CSAIL (MIT)
From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Courtney Haswell <courtneyhaswell@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Wednesday, August 12, 2020 at 09:34
To: "freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] hippocampal subfields error
External Email - Use Caution
We are getting an error after running the hippocampal subfields pipeline that we have never received before. It is happening for all subjects. We run recon-all and then the hippocampal pipeline and the output files are not being created.
Below is the beginning of the log and it seems like the relevant part is "This file does not contain MRI parameters" when referring to the imageDump file. I was able to open that file and it seems ok. What could be the problem? Thank you!
#--------------------------------------------
#@# Hippocampal Subfields processing (T1 only) left Mon Aug 10 18:54:21 EDT 2020
------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/packages/freesurfer_v6.0.0/MCRv80/runtime/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/bin/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/os/glnxa64:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/native_threads:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/server:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64/client:/usr/local/packages/freesurfer_v6.0.0/MCRv80/sys/java/jre/glnxa64/jre/lib/amd64:/usr/lib64/qt5/plugins/platforms:/usr/local/packages/ants-2.3.4/lib:/usr/lib64/openmpi/lib:
Warning: application is running on a locale different from the original platform locale.
Warning: No display specified. You will not be able to display graphics on the screen.
Registering imageDump.mgz to hippocampal mask from ASEG
This file does not contain MRI parameters
$Id: mri_robust_register.cpp,v 1.77 2016/01/20 23:36:17 greve Exp $
--mov: Using imageDump.mgz as movable/source volume.
--dst: Using /mnt/BIAC/.users/ch186/duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz
as target volume.
--lta: Output transform as trash.lta .
--mapmovhdr: Will save header adjusted movable as imageDump_coregistered.mgz !
--sat: Using saturation 50 in M-estimator!
reading source 'imageDump.mgz'...
reading target '/mnt/BIAC/.users/ch186/duhsnas-pri.dhe.duke.edu/dusom_morey/Data/Lab/PGC/T1s/Duke_data/Freesurfer/addl/cch/12588326/tmp/hippoSF_T1_v10_left//hippoAmygBinaryMask_autoCropped.mgz'...