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 <corinna...@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 <gr...@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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