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
>>
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>>
>>
>>
>>
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