Hi Morgan, this is a problem with newer versions of csh -- they changed the way that errors are reported. Try using this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/reg-feat2anat doug On 7/28/13 10:00 AM, Bruce Fischl wrote: > Hi Morgan > that is odd. I think Doug is traveling which may slow down his normal > rapid response time. > Bruce > > On Sat, 27 Jul 2013, Morgan Hough wrote: > >> Hi there, >> >> I am trying to run reg-feat2anat and having a bit of an odd problem. It runs >> but doesn't produce a anat2exf.register.dat. If I look at the >> anat2exf.register.dat.fslregister.log file I see right at the beginning it >> fail with: >> >> /data/results/genDIS >> mri_convert ERROR: could not determine file for > /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: > /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii >> mri_convert ERROR: could not determine file for >> /data/freesurfer_recons/HierGENDIS/WaisgenDIS600/mri/ERROR: >> /data/results/genDIS/WaisgenDIS600/gendistask_full_search.feat/reg/freesurfer/tmp/refvol.fslregister.nii >> >> mri_convert: extra arguments ("not" and following) >> >> type mri_convert -u for usage >> >> This is running on a SGE cluster using Ubuntu 12.04.1, FreeSurfer 5.3 and >> FSL 5.0.4 which made me think it is is similar to Sal's problem recently. So >> I added "set fsvol = brainmask" and that seems to have fixed it. Is there a >> different fix I can make to solve this? >> >> Cheers, >> >> -Morgan >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ 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.
