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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-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas N. Greve dgreve@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:
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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-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de falk.luesebrink@med.ovgu.demailto:falk.luesebrink@med.ovgu.de Sent: Thursday, May 5, 2022 4:17 AM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: [External] Re: [Freesurfer] Reversing mri_convert
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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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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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