Hello FreeSurfer users,
I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this:
1) bbregister --s sub-01 --mov ./MD.mni152.nii --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix
2) mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space
Thanks in advance,
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
External Email - Use Caution
I would probably run recon-all on the mni152, and then sample the MD map onto the mni152 surface, then use mris_apply_reg to map it to an individual. Also, Thomas Yeo has some possibly-better tools to do this.
On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:
Hello FreeSurfer users,
I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this:
- bbregister --s sub-01 --mov ./MD.mni152.nii --reg
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix
- mri_vol2vol --mov ./MD.mni152.nii --targ
$SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space
Thanks in advance,
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
External Email - Use Caution
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug!
When you say sample onto the mni152 surface, you mean to use mri_vol2surf, correct?
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
On May 27, 2020, at 11:10 AM, Douglas N. Greve dgreve@mgh.harvard.edu wrote:
I would probably run recon-all on the mni152, and then sample the MD map onto the mni152 surface, then use mris_apply_reg to map it to an individual. Also, Thomas Yeo has some possibly-better tools to do this.
On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:
Hello FreeSurfer users,
I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this:
bbregister --s sub-01 --mov ./MD.mni152.nii --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix
mri_vol2vol --mov ./MD.mni152.nii --targ $SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space
Thanks in advance,
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
External Email - Use Caution
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Correct. Also make sure to set --projfrac 0.5 to sample in the middle of cortex (or set to some other value depending upon where you want to sample)
On 5/27/2020 3:12 PM, Nillo, Ryan Michael R wrote:
Thanks Doug!
When you say sample onto the mni152 surface, you mean to use mri_vol2surf, correct?
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
On May 27, 2020, at 11:10 AM, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> wrote:
I would probably run recon-all on the mni152, and then sample the MD map onto the mni152 surface, then use mris_apply_reg to map it to an individual. Also, Thomas Yeo has some possibly-better tools to do this.
On 5/27/2020 2:02 PM, Nillo, Ryan Michael R wrote:
Hello FreeSurfer users,
I have a mean diffusivity map that exists in MNI152 space that I want to register to a subject’s anatomical space. In the end, I want to display the diffusivity on the subject’s surface. I want to ask if this is the correct way to do this:
- bbregister --s sub-01 --mov ./MD.mni152.nii --reg
$SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --init-fsl —dti #create registration matrix
- mri_vol2vol --mov ./MD.mni152.nii --targ
$SUBJECTS_DIR/sub-01/mri/brain.mgz --reg $SUBJECTS_DIR/sub-01/mri/transforms/bbregister.dat --o ./MD.nii #register mean diffusivity map to subject space
Thanks in advance,
Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging
External Email - Use Caution
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Nillo, Ryan Michael R