Where did mni152.orig.mgz.reg come from? It is not produced by mni152reg ... doug
On 10/15/14 10:19 AM, Corinna Bauer 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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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