Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2
mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
However, I do not see anything on the sphere (or fsaverage for that matter) ...
Can you provide any hints?
The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ...
Any tips would be a big help!
Best wishes,
Jason.
First, make sure that the volume you created is in register with the template functional. Eg,
tkmedit -f f.nii -ov f_LH12.mgz
where f.nii is the functional that f_LH12.mgz was derived from.
Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header
The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject).
The tksurfer cmd is correct, just make sure to use the correct subject.
doug
Jason Connolly wrote:
Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header —t2
mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
However, I do not see anything on the sphere (or fsaverage for that matter) …
Can you provide any hints?
The phase values are normalized and range from 4 – 5 and I have converted to RAS space properly (I hope) …
Any tips would be a big help!
Best wishes,
Jason.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thank you for your advice Doug.
Best wishes,
-jason.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 09 February 2011 16:42 To: Jason Connolly Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] phase data overlay using fsaverage
First, make sure that the volume you created is in register with the template functional. Eg,
tkmedit -f f.nii -ov f_LH12.mgz
where f.nii is the functional that f_LH12.mgz was derived from.
Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header
The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject).
The tksurfer cmd is correct, just make sure to use the correct subject.
doug
Jason Connolly wrote:
Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2
mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
However, I do not see anything on the sphere (or fsaverage for that matter) ...
Can you provide any hints?
The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ...
Any tips would be a big help!
Best wishes,
Jason.
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Dear Doug,
Thank you! I was able to display on the freesurfer surface from a matlab array to surface pipeline.
However, only a portion of my voxels showed up on the surface, presumable owing that the others fall in the white matter ...
My question is: is there any way to override this so that all the voxels are 'forced' to display on the surface?
Many thanks,
Jason.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 09 February 2011 16:42 To: Jason Connolly Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] phase data overlay using fsaverage
First, make sure that the volume you created is in register with the template functional. Eg,
tkmedit -f f.nii -ov f_LH12.mgz
where f.nii is the functional that f_LH12.mgz was derived from.
Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header
The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject).
The tksurfer cmd is correct, just make sure to use the correct subject.
doug
Jason Connolly wrote:
Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2
mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
However, I do not see anything on the sphere (or fsaverage for that matter) ...
Can you provide any hints?
The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ...
Any tips would be a big help!
Best wishes,
Jason.
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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.
Hi Jason
you can't get all the voxels onto the surface, as the surface is a 2D sheet cutting through a 3D volume. This is actually one of the big advantages of surface-based analysis as you avoid most of the regions that shouldn't have signal (e.g. ventricles, white matter, etc...). That said, there are some options in mri_vol2surf you can explore for changing the way you project from volume to surface. Check out Doug's excellent help.
cheers Bruce
On Thu, 10 Feb 2011, Jason Connolly wrote:
Dear Doug,
Thank you! I was able to display on the freesurfer surface from a matlab array to surface pipeline.
However, only a portion of my voxels showed up on the surface, presumable owing that the others fall in the white matter ...
My question is: is there any way to override this so that all the voxels are 'forced' to display on the surface?
Many thanks,
Jason.
-----Original Message----- From: Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] Sent: 09 February 2011 16:42 To: Jason Connolly Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: Re: [Freesurfer] phase data overlay using fsaverage
First, make sure that the volume you created is in register with the template functional. Eg,
tkmedit -f f.nii -ov f_LH12.mgz
where f.nii is the functional that f_LH12.mgz was derived from.
Once that is correct, run bbregister with the actual subject as the target (not fsaverage), spec the --mov as f.nii, and use --init-fsl instead of --init-header
The vol2surf cmd is correct, though it will sample it on the subject's surface (not that of fsaverage; you can change this with --trgsubject).
The tksurfer cmd is correct, just make sure to use the correct subject.
doug
Jason Connolly wrote:
Dear freesurfer experts,
I have used the mri.vol and mri.analyzehdr.vol fields to encode my coordinates and phase values using MRIread and MRIwrite (f_LH12.mgz).
I then brought these data into freesurfer using the following:
bbregister --s fsaverage --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg register12.dat --bold --init-header -t2
mri_vol2surf --mov /Applications/freesurfer/subjects/fsaverage/mri/f_LH12.mgz --reg /Applications/freesurfer/subjects/fsaverage/surf/register12.dat --hemi lh --surf white --o /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
tksurfer fsaverage lh sphere --overlay /Applications/freesurfer/subjects/fsaverage/surf/LH12.mgh
However, I do not see anything on the sphere (or fsaverage for that matter) ...
Can you provide any hints?
The phase values are normalized and range from 4 - 5 and I have converted to RAS space properly (I hope) ...
Any tips would be a big help!
Best wishes,
Jason.
--
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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
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
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
Jason Connolly