On Wed, Oct 15, 2014 at 11:17 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

Sorry, I gave you a bad command line. Try this

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

doug

On 10/15/2014 10:33 AM, Corinna Bauer wrote:
> 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
> <greve@nmr.mgh.harvard.edu <mailto:greve@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
>> <corinnab83@gmail.com <mailto: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

>> <mailto: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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>>
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
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