When you run that bet command line outside of trac-all, does it give you the same error?
On Wed, 15 Feb 2012, Chris Watson wrote: > Here's output from mri_info: > [freesurfer@occipital dmri]$ mri_info lowb.nii.gz > Volume information for lowb.nii.gz > type: nii > dimensions: 96 x 96 x 56 > voxel sizes: 2.5000, 2.5000, 2.5000 > type: FLOAT (3) > fov: 240.000 > dof: 0 > xstart: -120.0, xend: 120.0 > ystart: -120.0, yend: 120.0 > zstart: -70.0, zend: 70.0 > TR: 1000.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle: 0.00 > degrees > nframes: 1 > PhEncDir: UNKNOWN > ras xform present > xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r = > 0.9450 > : x_a = 0.0000, y_a = 1.0000, z_a = 0.0000, c_a = > 31.8560 > : x_s = 0.0000, y_s = 0.0000, z_s = 1.0000, c_s = > 25.3936 > Orientation : LAS > Primary Slice Direction: axial > > voxel to ras transform: > -2.5000 0.0000 0.0000 120.9450 > 0.0000 2.5000 0.0000 -88.1440 > 0.0000 0.0000 2.5000 -44.6064 > 0.0000 0.0000 0.0000 1.0000 > > voxel-to-ras determinant -15.625 > > ras to voxel transform: > -0.4000 0.0000 0.0000 48.3780 > -0.0000 0.4000 -0.0000 35.2576 > -0.0000 -0.0000 0.4000 17.8426 > 0.0000 0.0000 0.0000 1.0000 > > It looks normal in fslview/freeview. > Chris > > Anastasia Yendiki wrote: >> 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. >> >> >> > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
