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:
- mni152reg --s MAE_06072013
- 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.
- 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?
- mni152reg the subject's structural into MNI space
- inverse transform the MNI in the the subject's T1 space
- Use bbregister to align the DTI to the T1 space
- inverse transform the MNI into DTI space using mri_vol2vol using the
registration from step 3?
Cheers,
Corinna
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