The ASL has a different vox2ras transform.
How did you register the ASL to the anatoical?
How did you convert the ASL to the anatomical space?
On 5/6/2022 4:47 PM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
/The output for the orig.mgz is: /
Volume information for orig.mgz
type: MGH
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: UCHAR (0)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 7.00 msec, TE: 0.00 msec, TI: 0.00 msec, flip angle:
0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -1.0000, y_r = 0.0000, z_r = 0.0000, c_r =
2.6149
: x_a = 0.0000, y_a = 0.0000, z_a = 1.0000, c_a =
18.2086
: x_s = 0.0000, y_s = -1.0000, z_s = 0.0000, c_s =
4.6564
talairach xfm :
/home/victor/Processing/Finished_dev2019/25570_S4131FQU_SENSE/mri/transforms/talairach.xfm
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-1.0000 0.0000 0.0000 130.6149
0.0000 0.0000 1.0000 -109.7914
0.0000 -1.0000 0.0000 132.6564
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-1.0000 0.0000 -0.0000 130.6149
-0.0000 -0.0000 -1.0000 132.6564
0.0000 1.0000 0.0000 109.7914
-0.0000 -0.0000 -0.0000 1.0000
/I use mri_convert to create a .nii. I have an ASL image that is
registered exactly like it. Here is the output for the asl nifti. /
Volume information for test.nii.gz
type: nii
dimensions: 256 x 256 x 256
voxel sizes: 1.000000, 1.000000, 1.000000
type: FLOAT (3)
fov: 256.000
dof: 0
xstart: -128.0, xend: 128.0
ystart: -128.0, yend: 128.0
zstart: -128.0, zend: 128.0
TR: 9345.59 msec, TE: 0.00 msec, TI: 0.00 msec, flip
angle: 0.00 degrees
nframes: 1
PhEncDir: UNKNOWN
FieldStrength: 0.000000
ras xform present
xform info: x_r = -0.9990, y_r = 0.0435, z_r = -0.0046, c_r =
1.8094
: x_a = -0.0217, y_a = -0.4021, z_a = 0.9153, c_a =
-11.3674
: x_s = -0.0379, y_s = -0.9145, z_s = -0.4027, c_s =
-9.1954
Orientation : LIA
Primary Slice Direction: coronal
voxel to ras transform:
-0.9990 0.0435 -0.0046 124.7114
-0.0217 -0.4021 0.9153 -74.2729
-0.0379 -0.9145 -0.4027 164.2693
0.0000 0.0000 0.0000 1.0000
voxel-to-ras determinant -1
ras to voxel transform:
-0.9990 -0.0217 -0.0379 129.2118
0.0435 -0.4021 -0.9145 114.9404
-0.0046 0.9153 -0.4027 134.7101
-0.0000 -0.0000 -0.0000 1.0000
Transforming the test.nii.gz into a mgz loses its registration to do
the orig.mgz.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Douglas N. Greve
<dgr...@mgh.harvard.edu>
*Sent:* Thursday, May 5, 2022 4:36 PM
*To:* freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
*Subject:* [External] Re: [Freesurfer] Reversing mri_convert
What does "isn't displaying the same i/j/k ras" mean? In what tool?
What is the result of running mri_info on each volume?
On 5/5/2022 4:54 AM, Zeng, Victor (BIDMC - Keshavan - Psychiatry) wrote:
External Email - Use Caution
For some reason it isn't displaying the same i/j/k ras. The T1 and
the registered image (ASL) is in the same dimension/voxel sizes. The
TR is different at 7ms (T1) vs ~9000ms (ASL). When I try mri_convert
-tr 7 asl.nii asl.mgz, it doesn't change the incorrect i/j/k ras matrix
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
--
------------------------------------------------------------------------
*From:* freesurfer-boun...@nmr.mgh.harvard.edu
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu>
<freesurfer-boun...@nmr.mgh.harvard.edu>
<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of
falk.luesebr...@med.ovgu.de <mailto:falk.luesebr...@med.ovgu.de>
<falk.luesebr...@med.ovgu.de> <mailto:falk.luesebr...@med.ovgu.de>
*Sent:* Thursday, May 5, 2022 4:17 AM
*To:* freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
<freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu>
*Subject:* [External] Re: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi Victor,
in case you used mri_convert like this only, there is no change in
orientation or spacing between orig.mgz and T1.nii. So, whatever you
registered to the T1.nii should also be in space of the orig.mgz.
Best,
Falk
...............................................
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<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> im Auftrag von Zeng,
Victor (BIDMC - Keshavan - Psychiatry) <vz...@bidmc.harvard.edu>
<mailto:vz...@bidmc.harvard.edu>
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>
Betreff: [Freesurfer] Reversing mri_convert
External Email - Use Caution
Hi,
I convert orig.mgz -> T1.nii using mri_convert orig.mgz T1.nii
I now have something registered to the T1.nii and would like to move
it back to Freesurfer space. How would you go about doing that? I am
assuming I would do the inverse of the mri_convert, but I can't seem
to find the option to write the matrix.
Victor Zeng
Beth Israel Deaconess Medical Center
Keshavan Lab
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