Thanks Doug, now it is working perfectly!
On Fri, Dec 13, 2013 at 6:05 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>wrote: > > 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/ > >
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