Re: [Freesurfer] Transform labels in Diffusion space into MNI space

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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the e-mail
contains patient information, please contact the Partners
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you in error
but does not contain patient information, please contact the
sender and properly
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