On Fri, Dec 13, 2013 at 6:05 PM, Douglas N Greve <greve@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 <greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@nmr.mgh.harvard.edu <mailto:greve@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
greve@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/