Hey Chris - That is strange. The FSLOUTPUTTYPE would've been my first guess, too. Does this lowb.nii.gz actually exist? Anything looks strange when you run mri_info/freeview/fslview on it?
a.y On Wed, 15 Feb 2012, Chris Watson wrote: > Hello, in running trac-all -prep, I get an error saying that it can't > open "lowb.nii.gz.hdr": > > fslroi > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/dwi.nii.gz > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > 0 1 > fslmaths > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > -Tmean > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > bet > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb_brain.nii.gz > -m -f 0.3 > Can't open > /raid2/fmri8/fontan/volumetric/freesurfer/1.5T/cardiac/foo_b/dmri/lowb.nii.gz.hdr > Linux occipital.tch.harvard.edu 2.6.18-274.17.1.el5 #1 SMP Tue Jan 10 > 17:25:58 EST 2012 x86_64 x86_64 x86_64 GNU/Linux > > trac-preproc exited with ERRORS at Wed Feb 15 15:15:52 EST 2012 > > The variable FSLOUTPUTTYPE is set to NIFTI_GZ. I don't encounter this > problem with other subjects that I am processing. Any thoughts? > > Thanks, > Chris > > _______________________________________________ > 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.
