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This was part of an independent ASL pipeline called ExploreASL. 

I do not know 100% the details, but in short the orig.mgz was converted to a .nii through mri_convert for CAT12 and was registered to some native space, the deformation field was saved into some y_T1.nii (SPM). The ASL map was likewise registered to this native space.  I used SPM to revert the ASL map to the original T1 space (which works) using the y_T1.nii. Some intermediate reslicing steps were done as well to get it to a certain dimension. I will get back to you with further details as I inquire

Is this something that has an easy fix? 

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 12, 2022 3:38 PM
To: freesurfer@nmr.mgh.harvard.edu <freesurfer@nmr.mgh.harvard.edu>
Subject: [External] Re: [Freesurfer] [External] Re: Reversing mri_convert
 
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-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
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
--
        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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Von: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> im Auftrag von Zeng, Victor (BIDMC - Keshavan - Psychiatry) <vzeng@bidmc.harvard.edu>
Gesendet: Donnerstag, 5. Mai 2022 10:09:26
An: 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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