Hi, I am trying to register a volumetric roi from an average subject that I created to each individual subject's functional space. I have the transformation matrices that I applied to the functional data to bring them into the average space. When I apply the inverse of those transforms to the roi, the results are way off so I think I must be missing something.
1. I created a volume from a label with mri_label2vol. 2. I map the volume in the average space to the native functional space with mri_vol2vol.
I take it this is not correct and would appreciate any guidance. Thank you, pb
What is the average subject? How did you compute the registration between the average subject volume and the individual?
On 05/10/2016 01:37 PM, Patrick Beukema wrote:
Hi, I am trying to register a volumetric roi from an average subject that I created to each individual subject's functional space. I have the transformation matrices that I applied to the functional data to bring them into the average space. When I apply the inverse of those transforms to the roi, the results are way off so I think I must be missing something.
- I created a volume from a label with mri_label2vol.
- I map the volume in the average space to the native functional
space with mri_vol2vol.
I take it this is not correct and would appreciate any guidance. Thank you, pb
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The average subject is the average of my own subjects (18). I registered each individual subject's functional data to the average subject with spm_register.
On Tue, May 10, 2016 at 5:43 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
What is the average subject? How did you compute the registration between the average subject volume and the individual?
On 05/10/2016 01:37 PM, Patrick Beukema wrote:
Hi, I am trying to register a volumetric roi from an average subject that I created to each individual subject's functional space. I have the transformation matrices that I applied to the functional data to bring them into the average space. When I apply the inverse of those transforms to the roi, the results are way off so I think I must be missing something.
- I created a volume from a label with mri_label2vol.
- I map the volume in the average space to the native functional
space with mri_vol2vol.
I take it this is not correct and would appreciate any guidance. Thank you, pb
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
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Register your average subject to each individual with mri_coreg (see below) using --s subject --dof 12, then use mri_label2vol with --seg ROI.nii.gz to map the ROI into the individual space. If the ROI is surface-based, then you could recon-all your average, map the ROI to the surface with mri_vol2surf, then to the individual subject with mri_surf2surf
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
On 5/11/16 9:40 AM, Patrick Beukema wrote:
The average subject is the average of my own subjects (18). I registered each individual subject's functional data to the average subject with spm_register.
On Tue, May 10, 2016 at 5:43 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
What is the average subject? How did you compute the registration between the average subject volume and the individual? On 05/10/2016 01:37 PM, Patrick Beukema wrote: > Hi, > I am trying to register a volumetric roi from an average subject that > I created to each individual subject's functional space. I have the > transformation matrices that I applied to the functional data to bring > them into the average space. When I apply the inverse of those > transforms to the roi, the results are way off so I think I must be > missing something. > > 1. I created a volume from a label with mri_label2vol. > 2. I map the volume in the average space to the native functional > space with mri_vol2vol. > > I take it this is not correct and would appreciate any guidance. > Thank you, > pb > > > _______________________________________________ > 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 <tel:617-724-2358> Fax: 617-726-7422 <tel: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.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks very much. That did it. PB
On Wed, May 11, 2016 at 10:27 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
Register your average subject to each individual with mri_coreg (see below) using --s subject --dof 12, then use mri_label2vol with --seg ROI.nii.gz to map the ROI into the individual space. If the ROI is surface-based, then you could recon-all your average, map the ROI to the surface with mri_vol2surf, then to the individual subject with mri_surf2surf
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_coreg
On 5/11/16 9:40 AM, Patrick Beukema wrote:
The average subject is the average of my own subjects (18). I registered each individual subject's functional data to the average subject with spm_register.
On Tue, May 10, 2016 at 5:43 PM, Douglas N Greve < greve@nmr.mgh.harvard.edu> wrote:
What is the average subject? How did you compute the registration between the average subject volume and the individual?
On 05/10/2016 01:37 PM, Patrick Beukema wrote:
Hi, I am trying to register a volumetric roi from an average subject that I created to each individual subject's functional space. I have the transformation matrices that I applied to the functional data to bring them into the average space. When I apply the inverse of those transforms to the roi, the results are way off so I think I must be missing something.
- I created a volume from a label with mri_label2vol.
- I map the volume in the average space to the native functional
space with mri_vol2vol.
I take it this is not correct and would appreciate any guidance. Thank you, pb
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 mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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
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Douglas Greve -
Douglas N Greve
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Patrick Beukema