I'm not sure what is in that file.  Try doing it the way that I suggested and see if it works.
doug

On 10/15/14 10:29 AM, Corinna Bauer wrote:

Doug, instead of using the register.dat (which was generated from bbregister --s ${subject} --mov ${dti_file} --dti --init-fsl --reg register.dat), I had to use the registration file generated from the mri_vol2vol step where the orig T1 is put into dti space:
    mri_vol2vol --mov ${dti_file} --targ ${subj_dir}/mri/orig.mgz --reg register.dat --inv --o ${mri_indtispace}.

mri_matrix_multiply -im MAE_06072013/mri/mni152.orig.mgz.reg -iim MAE_06072013/mri_indtispace.nii.reg -om MAE_06072013/newmnireg.dat

Corinna

On Wed, Oct 15, 2014 at 10:19 AM, Corinna Bauer <corinnab83@gmail.com> 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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