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 _______________________________________________ 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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