hey doug, fslregister already uses flirt.fsl from freesurfer. you only need to provide the schedule file and update the path. i just ran it copying the schedule file over from fsl to a new location and setting the environment variable FSLDIR, which i presume could be replaced with FREESURFER_HOME. things ran fine to completion.
cheers, satra On Fri, Jul 5, 2013 at 2:14 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > 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 <sa...@mit.edu <mailto: >> 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 >> <mailto:gr...@nmr.mgh.harvard.**edu<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<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<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:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> > https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/** >> freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@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> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<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> >> >> <http://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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu> >> > >> >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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<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. >> >> >> >> > -- > 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<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<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/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > >
_______________________________________________ Freesurfer mailing list 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.
