Hi Doug, That still gives sag rotated -90 degrees, axial shows up as a coronal rotated 180 deg, and coronal shows up as axial.
Corinna On Wed, Oct 15, 2014 at 11:17 AM, Douglas N Greve <gr...@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 > > <gr...@nmr.mgh.harvard.edu <mailto: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 <mailto: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 > >> <mailto: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 > >>> > >>> > >>> _______________________________________________ > >>> 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. > >> > >> > >> > >> > >> > >> _______________________________________________ > >> 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. > > > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >
_______________________________________________ Freesurfer mailing list 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.
