Run tkregister2 --mov MEG_ROI.nii --targ path/to/spm8/canonical/single_subj_T1.nii --regheader --reg reg1.dat mri_matrix_multiply -im reg1.dat -im Mikel_SingleSubject_to_Colin.dat -om final.reg.dat Then use final.reg.dat
doug On 12/13/2013 11:56 AM, Garikoitz Lerma-Usabiaga wrote: > Hi Doug, > this is what I did. This system worked in other occasions. Could it be > the problem how the volume MEG_ROI.nii was created? My colleague had a > Matlab matrix of 256x256x256 and he converted it to a .nii file. > > The registration matrix between single_subj_T1.nii and Colin27 is the > following one: > > Colin > > 2.000000 > > 2.000000 > > 0.150000 > > 9.999982714653015e-01 -1.096551306545734e-03 -1.517703873105347e-03 > 5.575752854347229e-01 > > 1.516161020845175e-03 -1.406581024639308e-03 9.999977946281433e-01 > -1.579373359680176e+00 > > -1.098683569580317e-03 -9.999984502792358e-01 -1.404915703460574e-03 > 6.750410795211792e-01 > > 0 0 0 1 > > round > > (obtained with: bbregister --s Colin --mov > path/to/spm8/canonical/single_subj_T1.nii--init-spm --reg > from_SingleSubject_to_Colin.dat --t1) > > > > Can you recommend anything to try now? > > > thanks! > > Gari > > > > On Fri, Dec 13, 2013 at 5:51 PM, Douglas N Greve > <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: > > Try registering path/to/spm8/canonical/single_subj_T1.nii to Colin > with > bbregister > doug > > > On 12/13/2013 11:09 AM, Garikoitz Lerma-Usabiaga wrote: > > Hi list, > > I am trying to visualize a .nii ROI coming from MEG, which is in > > Colin27 space. > > > > I can visualize it perfectly in mricron and tkmedit with the > following > > command: > > tkmedit -f path/to/spm8/canonical/single_subj_T1.nii -overlay > > MEG_ROI.nii -fthresh 0.5 > > (single_subj_T1.nii is Colin27) > > > > but when I visualize it with: > > > > tkmedit Colin T1.mgz -overlay ./rC_vs_D_band1_0.01_left.nii > > -overlay-reg > > > > /home/glerma/glerma/GIT/bcblscripts/FREESURFER/ROI/Mikel_SingleSubject_to_Colin.dat > > -fthresh 0.5 -surface lh.white -aux-surface rh.white > > > > > > > > The result is wrong, and different from the first tkmedit. > > > > > > Should I convert the MEG_ROI.nii ni some specific way to make it > work? > > Any suggestions? > > > > > > Thanks, > > > > Gari > > > > > > The registration matrix between single_subj_T1.nii and Colin27 > is the > > following one: > > > > Colin > > > > 2.000000 > > > > 2.000000 > > > > 0.150000 > > > > 9.999982714653015e-01 -1.096551306545734e-03 -1.517703873105347e-03 > > 5.575752854347229e-01 > > > > 1.516161020845175e-03 -1.406581024639308e-03 9.999977946281433e-01 > > -1.579373359680176e+00 > > > > -1.098683569580317e-03 -9.999984502792358e-01 -1.404915703460574e-03 > > 6.750410795211792e-01 > > > > 0 0 0 1 > > > > round > > > > (obtained with: bbregister --s Colin --mov > > path/to/spm8/canonical/single_subj_T1.nii--init-spm --reg > > from_SingleSubject_to_Colin.dat --t1) > > > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > <mailto: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 <mailto:gr...@nmr.mgh.harvard.edu> > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://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 <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. > > -- 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
