Hello,
I'm new to Freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is currently in MNI space (2mm). I would like to move this parcellation to subject native space, so that I can extract the BOLD timeseries from each region of the parcellation.
I understand that an option I have is to simply use FSL tools such as FLIRT or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job that just an affine transformation.
What should I do in this case?
1) Is there any freesurfer tool that would allow me to register a volume to another volume, but aided by surface information? 2) If so, what steps should I follow to extract BOLD timeseries for each subject from the parcellation regions?
Thank you very much,
-- Marcelo Mattar University of Pennsylvania
Hi Marcelo
you can use bbregister to register the surfaces to another volume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform)
cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote:
Hello, I'm new to Freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is currently in MNI space (2mm). I would like to move this parcellation to subject native space, so that I can extract the BOLD timeseries from each region of the parcellation.
I understand that an option I have is to simply use FSL tools such as FLIRT or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job that just an affine transformation.
What should I do in this case?
- Is there any freesurfer tool that would allow me to register a volume to
another volume, but aided by surface information? 2) If so, what steps should I follow to extract BOLD timeseries for each subject from the parcellation regions?
Thank you very much,
-- Marcelo Mattar University of Pennsylvania
Hi Bruce,
I'm chiming in because I've been having a similar issue with the method you mention above. Though, my goal is just to move the surface rendering into the subject's native space using tkregister2 and mri_surf2surf as suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
The problem I ran into is that the surface output from that procedure looks fine overlaid on the subject's native T1 in freeview (even if the original T1 was in LAS orientation). However, if I view the surface in any other viewer (e.g., in matlab using surf() or tripatch()), the surface is flipped left from right, and the frontal pole is facing down (what is usually ventral). I'm assuming freeview applies some transformation to orient it correctly, but I'm stumped there.
I was exchanging with Doug Greve about this and we couldn't figure it out. Any advice you might have is much appreciated.
Thanks for your help!
-zack
On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marcelo
you can use bbregister to register the surfaces to another volume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform)
cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote:
Hello, I'm new to Freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is
currently
in MNI space (2mm). I would like to move this parcellation to subject
native
space, so that I can extract the BOLD timeseries from each region of the parcellation.
I understand that an option I have is to simply use FSL tools such as
FLIRT
or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job
that
just an affine transformation.
What should I do in this case?
- Is there any freesurfer tool that would allow me to register a volume
to
another volume, but aided by surface information? 2) If so, what steps should I follow to extract BOLD timeseries for each subject from the parcellation regions?
Thank you very much,
-- Marcelo Mattar University of Pennsylvania
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.
Hi Zack
there is a ras2vox transform in the surface file header that I believe freeview uses. I'll cc Ruopeng so he can confirm and give you details
cheers Bruce On Mon, 13 Oct 2014, Zachary Greenberg wrote:
Hi Bruce, I'm chiming in because I've been having a similar issue with the method you mention above. Though, my goal is just to move the surface rendering into the subject's native space using tkregister2 and mri_surf2surf as suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
The problem I ran into is that the surface output from that procedure looks fine overlaid on the subject's native T1 in freeview (even if the original T1 was in LAS orientation). However, if I view the surface in any other viewer (e.g., in matlab using surf() or tripatch()), the surface is flipped left from right, and the frontal pole is facing down (what is usually ventral). I'm assuming freeview applies some transformation to orient it correctly, but I'm stumped there.
I was exchanging with Doug Greve about this and we couldn't figure it out. Any advice you might have is much appreciated.
Thanks for your help!
-zack
On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marcelo
you can use bbregister to register the surfaces to another volume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform) cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote: > Hello, > I'm new to Freesurfer, and I'm lost in something that I believe is very > basic. I have a parcellation of the brain in .nii format that is currently > in MNI space (2mm). I would like to move this parcellation to subject native > space, so that I can extract the BOLD timeseries from each region of the > parcellation. > > I understand that an option I have is to simply use FSL tools such as FLIRT > or FNIRT and move the parcellation file to subject space (using nearest > neighbor interpolation). However, given that I have reconstructed the > subject's anatomy to the surface space, I believe I can do a better job that > just an affine transformation. > > What should I do in this case? > > 1) Is there any freesurfer tool that would allow me to register a volume to > another volume, but aided by surface information? > 2) If so, what steps should I follow to extract BOLD timeseries for each > subject from the parcellation regions? > > Thank you very much, > > -- > Marcelo Mattar > University of Pennsylvania > > _______________________________________________ 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.
Yes, there is, and there is an adjustment made to the vox2ras so that freeview reads it properly. Still that should not affect the actual coordinates. However, if you want to use another viewer, you have to make sure that the coordinates are consistent between the volume and the surface. Just throwing it into another viewer is surely going to fail. The coordinates will be in tkregister-style XYZ in the target space. Look at our page on coordinate systems to see what that means.
doug
On 10/13/2014 06:28 PM, Bruce Fischl wrote:
Hi Zack
there is a ras2vox transform in the surface file header that I believe freeview uses. I'll cc Ruopeng so he can confirm and give you details
cheers Bruce On Mon, 13 Oct 2014, Zachary Greenberg wrote:
Hi Bruce, I'm chiming in because I've been having a similar issue with the method you mention above. Though, my goal is just to move the surface rendering into the subject's native space using tkregister2 and mri_surf2surf as suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat
The problem I ran into is that the surface output from that procedure looks fine overlaid on the subject's native T1 in freeview (even if the original T1 was in LAS orientation). However, if I view the surface in any other viewer (e.g., in matlab using surf() or tripatch()), the surface is flipped left from right, and the frontal pole is facing down (what is usually ventral). I'm assuming freeview applies some transformation to orient it correctly, but I'm stumped there.
I was exchanging with Doug Greve about this and we couldn't figure it out. Any advice you might have is much appreciated.
Thanks for your help!
-zack
On Sat, Oct 11, 2014 at 2:04 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi Marcelo
you can use bbregister to register the surfaces to anothervolume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform)
cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote: > Hello, > I'm new to Freesurfer, and I'm lost in something that Ibelieve is very > basic. I have a parcellation of the brain in .nii format that is currently > in MNI space (2mm). I would like to move this parcellation to subject native > space, so that I can extract the BOLD timeseries from each region of the > parcellation. > > I understand that an option I have is to simply use FSL tools such as FLIRT > or FNIRT and move the parcellation file to subject space (using nearest > neighbor interpolation). However, given that I have reconstructed the > subject's anatomy to the surface space, I believe I can do a better job that > just an affine transformation. > > What should I do in this case? > > 1) Is there any freesurfer tool that would allow me to register a volume to > another volume, but aided by surface information? > 2) If so, what steps should I follow to extract BOLD timeseries for each > subject from the parcellation regions? > > Thank you very much, > > -- > Marcelo Mattar > University of Pennsylvania > > _______________________________________________ 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 personto 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
Hi Bruce,
Thanks for your response. A couple of follow-ups:
1) Is using bbregister usually better than using FLIRT? After all, isn't it simply an affine transformation? 2) If I want to move my parcellation from MNI_2mm space to subject native space, shoud I use the MNI_2mm template as my input/movable volume and my SubjID as my subject? 3) What about cvs_register? Will I get a better registration outcome if I use this as opposed to bbregister, followed by mri_vol2vol?
Thank you very much, Bruce!
-- Marcelo
On Sat, Oct 11, 2014 at 5:04 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi Marcelo
you can use bbregister to register the surfaces to another volume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform)
cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote:
Hello, I'm new to Freesurfer, and I'm lost in something that I believe is very basic. I have a parcellation of the brain in .nii format that is
currently
in MNI space (2mm). I would like to move this parcellation to subject
native
space, so that I can extract the BOLD timeseries from each region of the parcellation.
I understand that an option I have is to simply use FSL tools such as
FLIRT
or FNIRT and move the parcellation file to subject space (using nearest neighbor interpolation). However, given that I have reconstructed the subject's anatomy to the surface space, I believe I can do a better job
that
just an affine transformation.
What should I do in this case?
- Is there any freesurfer tool that would allow me to register a volume
to
another volume, but aided by surface information? 2) If so, what steps should I follow to extract BOLD timeseries for each subject from the parcellation regions?
Thank you very much,
-- Marcelo Mattar University of Pennsylvania
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.
you should use the method I posted
On 10/15/2014 04:42 PM, Marcelo Mattar wrote:
Hi Bruce,
Thanks for your response. A couple of follow-ups:
- Is using bbregister usually better than using FLIRT? After all,
isn't it simply an affine transformation? 2) If I want to move my parcellation from MNI_2mm space to subject native space, shoud I use the MNI_2mm template as my input/movable volume and my SubjID as my subject? 3) What about cvs_register? Will I get a better registration outcome if I use this as opposed to bbregister, followed by mri_vol2vol?
Thank you very much, Bruce!
-- Marcelo
On Sat, Oct 11, 2014 at 5:04 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:
Hi Marcelo you can use bbregister to register the surfaces to another volume, and mri_vol2surf to then map the volume onto the surface (or mri_vol2vol to apply the volume transform) cheers Bruce On Sat, 11 Oct 2014, Marcelo Mattar wrote: > Hello, > I'm new to Freesurfer, and I'm lost in something that I believe is very > basic. I have a parcellation of the brain in .nii format that is currently > in MNI space (2mm). I would like to move this parcellation to subject native > space, so that I can extract the BOLD timeseries from each region of the > parcellation. > > I understand that an option I have is to simply use FSL tools such as FLIRT > or FNIRT and move the parcellation file to subject space (using nearest > neighbor interpolation). However, given that I have reconstructed the > subject's anatomy to the surface space, I believe I can do a better job that > just an affine transformation. > > What should I do in this case? > > 1) Is there any freesurfer tool that would allow me to register a volume to > another volume, but aided by surface information? > 2) If so, what steps should I follow to extract BOLD timeseries for each > subject from the parcellation regions? > > Thank you very much, > > -- > Marcelo Mattar > University of Pennsylvania > > _______________________________________________ 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.--
Marcelo Mattar http://about.me/marcelomattar
http://about.me/marcelomattar?promo=email_sig
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Douglas,
I don't know if I understand what method you're referring to. From your previous response, I only see a recommendation for a transform that freeview uses (ras2vox). What I'm interested in doing is just to move a parcellation file containing cortical and subcortical structures from MNI_2mm space into subject's EPI space.
Sorry if I'm misunderstanding something here.
-- Marcelo
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Douglas N Greve -
Marcelo Mattar -
Zachary Greenberg