Weird. Glad it got fixed, let us know if you have any more trouble. On Wed, 15 Feb 2012, Chris Watson wrote:
> Actually, it now works when I re-source my .bash_profile and .bashrc files. > Not sure why that would be. > Chris > > Chris Watson wrote: >> Yes, the same error. >> Chris >> >> Anastasia Yendiki wrote: >> >> > 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 >> >> > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
