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 endifcheers,
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 > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.