hi doug,

same error with the updated one when i don't have FSL installed.

writing to /data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii...

fslregister --s H0351.2002 --mov /data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/template.nii --re

g /data/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/reg.init.dat --niters 1 --maxangle 90 --tmp /dat

a/subjects/H0351.2002/mri/transforms/tmp.bbregister.7856/fslregister --dof 6 --fsvol brainmask.mgz --nobetmov

ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation

perhaps this is what's complaining in fslregister:

```

if($DoTrans) then

if($?FSLDIR == 0) then

echo "ERROR: you must have the FSLDIR environment variable defined and pointing to the FSL installation"

exit 1;

endif

if(! -e $FSLDIR/etc/flirtsch/xyztrans.sch) then

echo "ERROR: cannot find $FSLDIR/etc/flirtsch/xyztrans.sch"

exit 1;

endif

```

cheers,

satra

On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh <satra@mit.edu> wrote:

thanks doug, i'll try that version right now.

cheers,

satra

On Fri, Jul 5, 2013 at 11:37 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

I think the problem may be this:

WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh!

you can also update bbregister with the version here

ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/bbregister

doug

On 07/05/2013 09:55 AM, Satrajit Ghosh wrote:
> hi doug,
>
> bbregister was running into an error trying to do T2pial refinement
>
> sequence of commands and output here:
>
> https://gist.github.com/satra/5934639
>
> and it looks like the absence of FSLDIR
>
> i didn't have FSL installed on this machine - i thought that
> freesurfer had it's own version of flirt.
>
> is FSL necessary?
>
> cheers,
>
> satra
>
>
>

> _______________________________________________
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> Freesurfer@nmr.mgh.harvard.edu
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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