Hi Lars,
this test is too sensitive in FS5.3 . We have changed that a while ago.
The mri_diff command should be
mri_diff --notallow-pix --notallow-geo ....
if that still shows a difference, something is different in the image
resolution and that could be a problem. Only differences in the
transformation matrices are no problem.
Best, Martin
On 04/22/2016 08:52 AM, Lars M. Rimol wrote:
Hi,
I'm running longitudinal recon-all
(freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0) on Ubuntu 14.04.4,
with three timepoints per subject. I get this warning about geometry
(please see below). All three images have been converted from dicom to
.mgz using mri_convert. From a previous question on the list from last
year, I get the impression this warning should not appear if all
images have been transformed the same way. I've pasted mri_info on
both images at the bottom of the e-mail. The transformation matrices
differ from timepoint to timepoint and I suspect this might be the
reason for the warning. Is this a cause for concern?
Thank you!
#@# Longitudinal Base Subject Creation fr. 22. april 09:07:47 +0200 2016
/media/lmr2/subjects/TBI/artifakt_qc/KT5065_base
mri_diff --notallow-pix
/media/lmr2/subjects/TBI/artifakt_qc/Kt5065_2/mri/rawavg.mgz
/media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz
Volumes differ in geometry row=1 col=4 diff=1.606422 (1.60642)
mri_diff --notallow-pix
/media/lmr2/subjects/TBI/artifakt_qc/kt5065_reskann_2/mri/rawavg.mgz
/media/lmr2/subjects/TBI/artifakt_qc/KT5065_1/mri/rawavg.mgz
Volumes differ in geometry row=1 col=4 diff=1.713524 (1.71352)
*******************************************************************************
WARNING: Image geometries differ across time, maybe due to aquisition
changes?
This can potentially bias a longitudinal study! Will continue
in 10s.
*******************************************************************************
---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------
Comparison using mri_info
[09:27 lmr@dmed4870] > mri_info KT5065_1/mri/orig/001.mgz
Volume information for KT5065_1/mri/orig/001.mgz
type: MGH
dimensions: 256 x 256 x 176
voxel sizes: 1.0000, 1.0000, 1.0000
type: SHORT (4)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -88.0, zend: 88.0
TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip
angle: 9.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r
= -0.5000
: x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a
= 0.0000
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s
= 0.0000
talairach xfm :
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0000 -0.0000 -1.0000 87.5000
-1.0000 -0.0000 -0.0000 128.0000
0.0000 -1.0000 0.0000 128.0000
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0000 -1.0000 -0.0000 128.0000
-0.0000 -0.0000 -1.0000 128.0000
-1.0000 0.0000 0.0000 87.5000
0.0000 0.0000 0.0000 1.0000
[09:27 lmr@dmed4870] > mri_info Kt5065_2/mri/orig/001.mgz
Volume information for Kt5065_2/mri/orig/001.mgz
type: MGH
dimensions: 256 x 256 x 176
voxel sizes: 1.0000, 1.0000, 1.0000
type: SHORT (4)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -88.0, zend: 88.0
TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip
angle: 9.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r
= -2.1064
: x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a
= -3.2129
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s
= -5.6225
talairach xfm :
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0000 -0.0000 -1.0000 85.8936
-1.0000 -0.0000 -0.0000 124.7871
0.0000 -1.0000 0.0000 122.3775
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0000 -1.0000 -0.0000 124.7871
-0.0000 -0.0000 -1.0000 122.3775
-1.0000 0.0000 0.0000 85.8936
0.0000 0.0000 0.0000 1.0000
[09:28 lmr@dmed4870] > mri_info kt5065_3/mri/orig/001.mgz
Volume information for kt5065_3/mri/orig/001.mgz
type: MGH
dimensions: 256 x 256 x 176
voxel sizes: 1.0000, 1.0000, 1.0000
type: SHORT (4)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -88.0, zend: 88.0
TR: 2300.00 msec, TE: 4.21 msec, TI: 996.00 msec, flip
angle: 9.00 degrees
nframes: 1
PhEncDir: UNKNOWN
ras xform present
xform info: x_r = -0.0000, y_r = -0.0000, z_r = -1.0000, c_r
= 1.2135
: x_a = -1.0000, y_a = -0.0000, z_a = -0.0000, c_a
= 8.4827
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s
= -11.9426
talairach xfm :
Orientation : PIL
Primary Slice Direction: sagittal
voxel to ras transform:
-0.0000 -0.0000 -1.0000 89.2135
-1.0000 -0.0000 -0.0000 136.4827
0.0000 -1.0000 0.0000 116.0574
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.0000 -1.0000 -0.0000 136.4827
-0.0000 -0.0000 -1.0000 116.0574
-1.0000 0.0000 0.0000 89.2135
0.0000 0.0000 0.0000 1.0000
sincerely yours,
Lars M. Rimol, PhD
Senior researcher,
Norwegian Advisory Unit for functional MRI
Department of Radiology,
St. Olav's University hospital,
7006 Trondheim,
Norway
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
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--
Martin Reuter, PhD
Assistant Professor of Radiology, Harvard Medical School
Assistant Professor of Neurology, Harvard Medical School
A.A.Martinos Center for Biomedical Imaging
Massachusetts General Hospital
Research Affiliate, CSAIL, MIT
Phone: +1-617-724-5652
Web : http://reuter.mit.edu
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