hi doug,

without hacking recon-all is there a way to avoid using FSL when using the T2pial flag?

cheers,

satra

#@# 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