I am interested in knowing what type of alignment goes into the last stage of the longitudinal pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find the warp?
in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet.
cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote:
I am interested in knowing what type of alignment goes into the last stage of the longitudinal pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find the warp?
Is the warp saved anywhere and where can I find it? Also is the warp compatible with FNIRT in any way. I am interested in combining warps together to reduce the number of re-sampling steps. Thank you so much in advanced
On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet.
cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote:
I am interested in knowing what type of alignment goes into the last
stage of the longitudinal
pipeline. Are each longitudinal time point non-linearly aligned to the
base image? If so can I find
the warp?
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Hi Aaron
we compute the warp and save it in the mri/transforms/talairach.m3z, but don't apply it (so don't require an extra resampling). I know we have some tools around to convert to ANTS format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!)
cheers Bruce
On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
Is the warp saved anywhere and where can I find it? Also is the warp compatible with FNIRT in any way. I am interested in combining warps together to reduce the number of re-sampling steps. Thank you so much in advanced
On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet.
cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote: > > I am interested in knowing what type of alignment goes into the last stage of the longitudinal > pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find > the warp? > >
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Thank you very much. Your last email gave me a lot to work with.
On Mon, Jan 15, 2018 at 9:18 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Aaron
we compute the warp and save it in the mri/transforms/talairach.m3z, but don't apply it (so don't require an extra resampling). I know we have some tools around to convert to ANTS format, but I'm not sure about fnirt. I'll cc MJ who may know (hi MJ!)
cheers Bruce
On Mon, 15 Jan 2018, Aaron Tanenbaum wrote:
Is the warp saved anywhere and where can I find it? Also is the warp
compatible with FNIRT in any way. I am interested in combining warps together to reduce the number of re-sampling steps. Thank you so much in advanced
On Mon, Jan 15, 2018 at 8:53 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: in the last stage there is a nonlinear atlas alignment that is specific to each timepoint. We are working on building a nonlinear base, but it is not distributed yet.
cheers Bruce On Sun, 14 Jan 2018, Aaron Tanenbaum wrote: > > I am interested in knowing what type of alignment goes into thelast stage of the longitudinal > pipeline. Are each longitudinal time point non-linearly aligned to the base image? If so can I find > the warp? > > _______________________________________________ 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.
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