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
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