I guess it is needed for fslregister. I suppose we could have it use the version of flirt that we distribute and also distribute the schedule files.
doug

On 07/05/2013 01:29 PM, Satrajit Ghosh wrote:

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
  endif
```

cheers,

satra

On Fri, Jul 5, 2013 at 1:05 PM, Satrajit Ghosh <satra@mit.edu <mailto: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 <mailto: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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        --
        Douglas N. Greve, Ph.D.
        MGH-NMR Center

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