#@# Refine Pial Surfs w/ T2/FLAIR Sat Sep 24 08:42:34 UTC 2016
bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2
Log file is /subjects/sub-01/mri/transforms/T2raw.dat.log
Sat Sep 24 08:42:35 UTC 2016
setenv SUBJECTS_DIR /subjects
cd /subjects/sub-01/scripts
/opt2/freesurfer/bin/bbregister --s sub-01 --mov /subjects/sub-01/mri/orig/T2raw.mgz --lta /subjects/sub-01/mri/transforms/T2raw.lta --init-fsl --T2
$Id: bbregister,v 1.49.2.3 2013/03/25 18:04:53 greve Exp $
Linux b62492e050ac 4.4.20-moby #1 SMP Thu Sep 8 21:27:34 UTC 2016 x86_64 GNU/Linux
FREESURFER_HOME /opt2/freesurfer
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
mri_convert /subjects/sub-01/mri/orig/T2raw.mgz /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from /subjects/sub-01/mri/orig/T2raw.mgz...
TR=2500.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-0.0675638, -0.9838, -0.166052)
j_ras = (0.119725, -0.173224, 0.977578)
k_ras = (0.990505, -0.0461684, -0.129489)
writing to /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii...
fslregister --s sub-01 --mov /subjects/sub-01/mri/transforms/tmp.bbregister.4836/template.nii --reg /subjects/sub-01/mri/transforms/tmp.bbregister.4836/reg.init.dat --niters 1 --maxangle 90 --nobetmov --tmp /subjects/sub-01/mri/transforms/tmp.bbregister.4836/fslregister --dof 6 --fsvol brainmask.mgz
ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation