I'm pretty sure it came from mni152reg. Here are the last few lines of the mni152 reg output:

Final tkRAS-to-tkRAS Matrix is:
1.013   0.045   0.047 -1.659;
0.062 -0.209 -1.043 -15.101;
-0.025   0.933 -0.227   33.122;
0.000   0.000   0.000   1.000;

Vox2Vox Matrix is:
2.025   0.094 -0.090   36.461;
-0.049 -0.455 -1.865   206.757;
-0.124   2.086 -0.418   23.848;
0.000   0.000   0.000   1.000;

Resampling
Output registration matrix is identity
INFO: writing registration to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.lta
transformed matrix:
1.000   0.000 -0.000 -1.566;
-0.000 -0.000 -1.000 -23.577;
0.000   1.000 -0.000   9.029;
0.000   0.000   0.000   1.000;
transformed matrix:
0.500   0.000   0.000 -18.500;
0.000   0.500   0.000 -9.500;
0.000   0.000   0.500 -18.500;
0.000   0.000   0.000   1.000;
INFO: writing registration matrix to /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg
To check registration, run:

tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg

mri_vol2vol done

On Wed, Oct 15, 2014 at 10:28 AM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg ...
doug
On 10/15/14 10:19 AM, Corinna Bauer wrote:
Hi Doug,

I'm not sure why, but the registration is off. In tkregister2, the "coronal" appears as an axial slice and vice versa, while the sagittal is rotated 90 degrees compared to the target. I did the following:
1. mni152reg --s MAE_06072013
2. tkregister2 --mov /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz --targ /usr/share/fsl/5.0/data/standard/MNI152_T1_2mm_brain.nii.gz --reg /drobo/Documents_corinna_linux/freesurfer_subjects/MAE_06072013/mri/mni152.orig.mgz.reg

3. tkregister2 --mov MAE_06072013/hardi/eddy_bet_MAE_06072013_hardi.nii.gz --reg MAE_06072013/register.dat --surf

Up until this point, everything looks good and well registered.

4. mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/register.dat -om MAE_06072013/newmnireg.dat

Corinna
On Tue, Oct 14, 2014 at 11:00 PM, Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:
Hi Corinna, once you do #1, you can concatenate the register.dat with the mni152.2mm.reg.dat like this

mri_matrix_multipy -im mnireg.dat -iim register.dat -o newreg.dat

Check
tkregister2 --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat

mri_vol2vol --mov dti.nii --targ $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz --reg newreg.dat --o dti.in.mni.nii

doug

On 10/14/14 2:57 PM, Corinna Bauer wrote:
Hello all,
I am wanting to put labels currently in diffusion space into MNI space. Does this make sense or is there a more straight forward way?

1. mni152reg the subject's structural into MNI space

2. inverse transform the MNI in the the subject's T1 space

3. Use bbregister to align the DTI to the T1 space

4. inverse transform the MNI into DTI space using mri_vol2vol using the registration from step 3?

Cheers,

Corinna
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