I tried your suggestion first and the registration was off, whereby the
axial and coronal were switched and sagittal was rotated 90 degrees.
Corinna
On Wed, Oct 15, 2014 at 10:31 AM, Douglas Greve <gr...@nmr.mgh.harvard.edu>
wrote:
>
> 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 <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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>
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