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 )
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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.eduwrote:
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
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.
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.
Thanks Doug, now it is working perfectly!
On Fri, Dec 13, 2013 at 6:05 PM, Douglas N Greve greve@nmr.mgh.harvard.eduwrote:
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.eduhttps://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/
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.eduwrote:
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 https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 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/
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.
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Garikoitz Lerma-Usabiaga