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
