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
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 <poortata@umich.edu
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
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:
- 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 <poortata@umich.edu mailto:poortata@umich.edu> 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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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 greve@nmr.mgh.harvard.edu 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:
- 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 <poortata@umich.edu mailto:poortata@umich.edu> 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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