[Freesurfer] applying manual freesurfer edits to warped brain image
Hi freesurfer experts, I have two T1 images from the same subject acquired at the same time point. One of the images is distortion corrected using a calibration phantom, put through the full freesurfer pipeline and then extensively manually edited. The uncorrected image has had zero processing. What I would like now is to have the freesurfer segmentations on the uncorrected image and preserve as much as possible the manual edits. In other words, I would like to warp the surface meshes already obtained on the distortion corrected image to the uncorrected image. Is there already a suggested method that is optimal for this purpose? Thanks in advance for any advice! -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.
Re: [Freesurfer] applying manual freesurfer edits to warped brain image
What format is the distortion field stored in? If you can get it into .m3z I believe we have tools to do what you want > On Nov 2, 2014, at 9:37 PM, David Grayson wrote: > > Hi freesurfer experts, > > I have two T1 images from the same subject acquired at the same time point. > One of the images is distortion corrected using a calibration phantom, put > through the full freesurfer pipeline and then extensively manually edited. > The uncorrected image has had zero processing. What I would like now is to > have the freesurfer segmentations on the uncorrected image and preserve as > much as possible the manual edits. In other words, I would like to warp the > surface meshes already obtained on the distortion corrected image to the > uncorrected image. Is there already a suggested method that is optimal for > this purpose? > > Thanks in advance for any advice! > > -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.
Re: [Freesurfer] applying manual freesurfer edits to warped brain image
Thanks Bruce, So I just need a warp field in .m3z format. Cool. As this distortion correction is proprietary, we don't actually get the warp fields, which is silly. But I was thinking since scanner distortions are subtle and coarse, it should be sufficient to nonlinearly register the two unsegmented images using a simple intensity-based volumetric registration at a coarse warp resolution. Would the mri_cvs_register tool be suitable for this if I supply the --step3 flag? Otherwise I am stuck with trying to go between Freesurfer and another set of tools. Thanks! -David Date: Sun, 2 Nov 2014 21:44:23 -0500 > From: Bruce Fischl > > Subject: Re: [Freesurfer] applying manual freesurfer edits to warped > brain image > To: Freesurfer support list > > > Message-ID: <35417931-ce03-4cb8-a30e-c1f34c174...@nmr.mgh.harvard.edu > > > Content-Type: text/plain; charset="us-ascii" > > What format is the distortion field stored in? If you can get it into .m3z > I believe we have tools to do what you want > > > > > On Nov 2, 2014, at 9:37 PM, David Grayson > wrote: > > > > Hi freesurfer experts, > > > > I have two T1 images from the same subject acquired at the same time > point. One of the images is distortion corrected using a calibration > phantom, put through the full freesurfer pipeline and then extensively > manually edited. The uncorrected image has had zero processing. What I > would like now is to have the freesurfer segmentations on the uncorrected > image and preserve as much as possible the manual edits. In other words, I > would like to warp the surface meshes already obtained on the distortion > corrected image to the uncorrected image. Is there already a suggested > method that is optimal for this purpose? > > > > Thanks in advance for any advice! > > > > -David > > ___ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- next part -- > An HTML attachment was scrubbed... > URL: > http://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/attachments/20141102/65628850/attachment-0001.html > ___ 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.
