Re: [Freesurfer] warping segmentations onto unprocessed brain
ok, great. so let's say I have a linear transformation or a full warp field to go between the freesurfer processed image and the unprocessed brain. is there a way that I can propagate onto the unprocessed image the entire freesurfer contents including the "mri" and "label" and everything else, using the warp? The processed image has extensive manual edits, so I basically just want to transfer everything over. Thanks Bruce! -David On Thu, Feb 26, 2015 at 6:05 AM, Bruce Fischl wrote: > Hi David > > yes, you can use bbregister to do the rigid alignment, then use it as > initialization for mri_nl_align. I would think you are better off doing the > surface recons and using cvs though. It's only computer time > > cheers > Bruce > > On Wed, 25 Feb 2015, David Grayson wrote: > > > Hey Bruce, > > Thanks for responding. I would actually prefer nonlinear. I did not > mention > > it, but the aseg data that I have is on a distortion-corrected T1 image, > > whereas the unprocessed image I want to warp onto is the same scan but > not > > corrected for distortion. The distortions are nonlinear. I was hoping > there > > might be a way to get a warp field to go between the two images without > > running both images through the recon-all pipeline. Are there any other > > possible tools? > > > > Thanks! > > -David > > > > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl < > fis...@nmr.mgh.harvard.edu> > > wrote: > > Is there any reason you need it to be nonlinear? I would think > > bbregister and mri_vol2vol would do the trick > > Cheers > > Bruce > > > > > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson > >wrote: > > > > > > Hi freesurfers, > > > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > > freesurfer-processed image to a separate (unprocessed) T1 image > > on the same subject. I would like to use a purely > > intensity-based nonlinear volumetric registration to do this, to > > save time and complication. I understand I can do this if I have > > a .m3z warp file. > > > > > > My question is, how can I get this warp file? I have tried > > using mri_cvs_register with the --step3 option, but that appears > > to only work after the surface-based registrations have been > > carried out. I haven't found another tool to do this yet. > > > > > > Are there any ideas? Thank you very much for your time. > > > > > > -David > > > ___ > > > Freesurfer mailing list > > > Freesurfer@nmr.mgh.harvard.edu > > > https://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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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.
Re: [Freesurfer] warping segmentations onto unprocessed brain
Hi David yes, you can use bbregister to do the rigid alignment, then use it as initialization for mri_nl_align. I would think you are better off doing the surface recons and using cvs though. It's only computer time cheers Bruce On Wed, 25 Feb 2015, David Grayson wrote: > Hey Bruce, > Thanks for responding. I would actually prefer nonlinear. I did not mention > it, but the aseg data that I have is on a distortion-corrected T1 image, > whereas the unprocessed image I want to warp onto is the same scan but not > corrected for distortion. The distortions are nonlinear. I was hoping there > might be a way to get a warp field to go between the two images without > running both images through the recon-all pipeline. Are there any other > possible tools? > > Thanks! > -David > > On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl > wrote: > Is there any reason you need it to be nonlinear? I would think > bbregister and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson >wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image > on the same subject. I would like to use a purely > intensity-based nonlinear volumetric registration to do this, to > save time and complication. I understand I can do this if I have > a .m3z warp file. > > > > My question is, how can I get this warp file? I have tried > using mri_cvs_register with the --step3 option, but that appears > to only work after the surface-based registrations have been > carried out. I haven't found another tool to do this yet. > > > > Are there any ideas? Thank you very much for your time. > > > > -David > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] warping segmentations onto unprocessed brain
Hey Bruce, Thanks for responding. I would actually prefer nonlinear. I did not mention it, but the aseg data that I have is on a distortion-corrected T1 image, whereas the unprocessed image I want to warp onto is the same scan but not corrected for distortion. The distortions are nonlinear. I was hoping there might be a way to get a warp field to go between the two images without running both images through the recon-all pipeline. Are there any other possible tools? Thanks! -David On Wed, Feb 25, 2015 at 8:29 PM, Bruce Fischl wrote: > Is there any reason you need it to be nonlinear? I would think bbregister > and mri_vol2vol would do the trick > Cheers > Bruce > > > > > On Feb 25, 2015, at 11:18 PM, David Grayson > wrote: > > > > Hi freesurfers, > > > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image on the same > subject. I would like to use a purely intensity-based nonlinear volumetric > registration to do this, to save time and complication. I understand I can > do this if I have a .m3z warp file. > > > > My question is, how can I get this warp file? I have tried using > mri_cvs_register with the --step3 option, but that appears to only work > after the surface-based registrations have been carried out. I haven't > found another tool to do this yet. > > > > Are there any ideas? Thank you very much for your time. > > > > -David > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://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 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.
Re: [Freesurfer] warping segmentations onto unprocessed brain
Is there any reason you need it to be nonlinear? I would think bbregister and mri_vol2vol would do the trick Cheers Bruce > On Feb 25, 2015, at 11:18 PM, David Grayson wrote: > > Hi freesurfers, > > I am hoping to warp an aparc+aseg.mgh file from a subject's > freesurfer-processed image to a separate (unprocessed) T1 image on the same > subject. I would like to use a purely intensity-based nonlinear volumetric > registration to do this, to save time and complication. I understand I can do > this if I have a .m3z warp file. > > My question is, how can I get this warp file? I have tried using > mri_cvs_register with the --step3 option, but that appears to only work after > the surface-based registrations have been carried out. I haven't found > another tool to do this yet. > > Are there any ideas? Thank you very much for your time. > > -David > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://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] warping segmentations onto unprocessed brain
Hi freesurfers, I am hoping to warp an aparc+aseg.mgh file from a subject's freesurfer-processed image to a separate (unprocessed) T1 image on the same subject. I would like to use a purely intensity-based nonlinear volumetric registration to do this, to save time and complication. I understand I can do this if I have a .m3z warp file. My question is, how can I get this warp file? I have tried using mri_cvs_register with the --step3 option, but that appears to only work after the surface-based registrations have been carried out. I haven't found another tool to do this yet. Are there any ideas? Thank you very much for your time. -David ___ 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.
