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 <sa...@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 <
> gr...@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
>> >
>> >
>> >
>> > _______________________________________________
>> > Freesurfer mailing list
>> > Freesurfer@nmr.mgh.harvard.edu
>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>> --
>> Douglas N. Greve, Ph.D.
>> MGH-NMR Center
>> gr...@nmr.mgh.harvard.edu
>> Phone Number: 617-724-2358
>> Fax: 617-726-7422
>>
>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>> www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>>
>> _______________________________________________
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>>
>>
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