On Mon, Jul 25, 2016 at 5:21 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

It looks like one of two things:

1. The files SUBJ_ID.nii.gz is corrupted. See if another tool (FSL, SPM, AFNI) can read the file

2. You have run out of disk space

On 7/24/16 10:52 AM, Fred Sampedro wrote:
Dear FS experts,

I've installed freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 and I'm trying to run bbregister to register a AV45-PET image to its corresponding FS processed T1 image. For that, I'm trying to run:

bbregister --s SUBJ_ID --mov SUBJ_PET --reg register.dat --init-fsl --t1

And I keep getting segfaults:

Log file is register.dat.log
dom jul 24 16:44:19 CEST 2016

$Id: bbregister,v 1.49 2011/03/06 23:38:41 greve Exp $
Linux fredlab 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
FREESURFER_HOME /usr/local/freesurfer
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii
mri_convert ./allpets/SUBJ_ID/SUBJ_ID.nii.gz ./tmp.bbregister.5353/template.nii
Segmentation fault (core dumped)

I have tried the same installation and command in two different computers and obtained the same segfault. I have also tried the same pipeline using instead the FS version freesurfer-Linux-centos4-stable-pub-v5.1.0.tar.gz and get the same result. I didn't have this issue using freesurfer 5.3, but I need to use 5.1 for an ongoing project.

I'm in an Ubuntu 14.04 LTS with 3.6GB of Memory, Processor Intel Core 2 Duo 3.0GHz, Graphics Intel Q45/Q43 OS type 64 bits.

Any help would be much appreciated,

Thanks a lot in advance,

Fred Sampedro
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