Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space

[Poortata Shirish Lalwani]

Thank you so much for your response. I tried the 3rd solution and used
--trgsubject fsaverage and that works like a charm.

Best,
Pia

On Tue, Jan 9, 2018 at 6:04 PM, Douglas N Greve 
wrote:

> You probably set up the FSFAST analysis to sample onto the fsaverage
> surface (in your mkanalysis-sess command). There are a couple of things
> you can do: 1. redo the FSFAST analysis using "self" instead of
> fsaverage. 2. map the beta.nii to the subject's native anatomy using
> mri_surf2surf, or 3. Run mri_vol2surf with --trgsubject fsaverge to have
> your MRS output in fsaverage space
>
>
> On 01/09/2018 03:00 PM, Poortata Shirish Lalwani wrote:
> > Hello Freesurfer experts,
> > We are obtaining MRS data and functional MRI data on two separate days
> > for each subject. We use structural scan obtained during both these
> > sessions for the freesurfer segmentation.
> > MRS scan gives us a binary mask (nii format) in the same space as the
> > structural image obtained during that particular scan. We want to use
> > this binary mask during the surface based functional MRI analysis.
> > I tried the following process to do this:
> > 1) Registered the structural image to orig.mgz using:
> > bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg
> > register.dat
> > 2) Applied the register.dat created by above process to the binary
> > mask to transform it into the orig.mgz space using:
> > mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg
> > --o gabarightmask.mgh --interp nearest
> > (When I overlay this mask on orig.mgz using freeview they appear in
> > the correct position.)
> > 3) I then converted the volume to surface space using mri_vol2surf.
> > mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg
> > myregister.dat --hemi rh
> > However the size of this mask created by mri_vol2surf process is
> > (145236vertices) different from the size of beta.nii (163842 vertices)
> > that is created using selxavg. Is one of the above steps wrong? How to
> > resolve this discrepancy?
> >
> > Best,
> > Pia
> >
> > On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani
> > > wrote:
> >
> > Hi,
> > We are obtaining MRS data and functional MRI data on two separate
> > days for each subject. We use structural scan obtained during both
> > these sessions for the freesurfer segmentation. MRS scan gives us
> > a binary mask (nii format) in the same space as the structural
> > image obtained during that particular scan. We want to use this
> > binary mask during the surface based functional MRI analysis. I am
> > not sure how to transform this binary mask to the surface space.
> > Is there a way to do this?
> >
> > Best,
> > Pia
> >
> >
> >
> >
> > ___
> > 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
> gr...@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
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> properly
> dispose of the e-mail.
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>
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addressed. If you believe this e-mail was sent to you in error and the e-mail
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Re: [Freesurfer] Using MRS voxel mask in freesurfer surface space

[Douglas N Greve]

You probably set up the FSFAST analysis to sample onto the fsaverage 
surface (in your mkanalysis-sess command). There are a couple of things 
you can do: 1. redo the FSFAST analysis using "self" instead of 
fsaverage. 2. map the beta.nii to the subject's native anatomy using 
mri_surf2surf, or 3. Run mri_vol2surf with --trgsubject fsaverge to have 
your MRS output in fsaverage space


On 01/09/2018 03:00 PM, Poortata Shirish Lalwani wrote:
> Hello Freesurfer experts,
> We are obtaining MRS data and functional MRI data on two separate days 
> for each subject. We use structural scan obtained during both these 
> sessions for the freesurfer segmentation.
> MRS scan gives us a binary mask (nii format) in the same space as the 
> structural image obtained during that particular scan. We want to use 
> this binary mask during the surface based functional MRI analysis.
> I tried the following process to do this:
> 1) Registered the structural image to orig.mgz using:
> bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg 
> register.dat
> 2) Applied the register.dat created by above process to the binary 
> mask to transform it into the orig.mgz space using:
> mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg 
> --o gabarightmask.mgh --interp nearest
> (When I overlay this mask on orig.mgz using freeview they appear in 
> the correct position.)
> 3) I then converted the volume to surface space using mri_vol2surf.
> mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg 
> myregister.dat --hemi rh
> However the size of this mask created by mri_vol2surf process is 
> (145236vertices) different from the size of beta.nii (163842 vertices) 
> that is created using selxavg. Is one of the above steps wrong? How to 
> resolve this discrepancy?
>
> Best,
> Pia
>
> On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani 
> > wrote:
>
> Hi,
> We are obtaining MRS data and functional MRI data on two separate
> days for each subject. We use structural scan obtained during both
> these sessions for the freesurfer segmentation. MRS scan gives us
> a binary mask (nii format) in the same space as the structural
> image obtained during that particular scan. We want to use this
> binary mask during the surface based functional MRI analysis. I am
> not sure how to transform this binary mask to the surface space.
> Is there a way to do this?
>
> Best,
> Pia
>
>
>
>
> ___
> 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
gr...@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/

___
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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] Using MRS voxel mask in freesurfer surface space

[Poortata Shirish Lalwani]

Hello Freesurfer experts,
We are obtaining MRS data and functional MRI data on two separate days for
each subject. We use structural scan obtained during both these sessions
for the freesurfer segmentation.
MRS scan gives us a binary mask (nii format) in the same space as the
structural image obtained during that particular scan. We want to use this
binary mask during the surface based functional MRI analysis.
I tried the following process to do this:
1) Registered the structural image to orig.mgz using:
bbregister --mov t1spgr.nii --s subject --t1 --init-fsl --reg register.dat
2) Applied the register.dat created by above process to the binary mask to
transform it into the orig.mgz space using:
mri_vol2vol --reg register.dat --mov gabarightxyz_mask.nii --fstarg --o
gabarightmask.mgh --interp nearest
(When I overlay this mask on orig.mgz using freeview they appear in the
correct position.)
3) I then converted the volume to surface space using mri_vol2surf.
mri_vol2surf --src gabarightmask.mgh --out gabarightsurf.nii --srcreg
myregister.dat --hemi rh
However the size of this mask created by mri_vol2surf process is (145236
vertices) different from the size of beta.nii (163842 vertices) that is
created using selxavg. Is one of the above steps wrong? How to resolve this
discrepancy?

Best,
Pia

On Mon, Jan 8, 2018 at 2:58 PM, Poortata Shirish Lalwani  wrote:

> Hi,
> We are obtaining MRS data and functional MRI data on two separate days for
> each subject. We use structural scan obtained during both these sessions
> for the freesurfer segmentation. MRS scan gives us a binary mask (nii
> format) in the same space as the structural image obtained during that
> particular scan. We want to use this binary mask during the surface based
> functional MRI analysis. I am not sure how to transform this binary mask to
> the surface space. Is there a way to do this?
>
> Best,
> Pia
>
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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
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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] Using MRS voxel mask in freesurfer surface space

[Poortata Shirish Lalwani]

Hi,
We are obtaining MRS data and functional MRI data on two separate days for
each subject. We use structural scan obtained during both these sessions
for the freesurfer segmentation. MRS scan gives us a binary mask (nii
format) in the same space as the structural image obtained during that
particular scan. We want to use this binary mask during the surface based
functional MRI analysis. I am not sure how to transform this binary mask to
the surface space. Is there a way to do this?

Best,
Pia
___
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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.