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Dear Doctor Iglesias,
Thanks for your previous reply. As agreed, I post my question on the Freesurfer list.
We are doing shape analyses on thalamus in order to determine whether distinct cognitive profiles in Parkinson’s disease have different deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape analysis module in Slicer4) to obtain deformation fields and p-values map (cf. attached file; vectors represent the magnitude of deformation between two groups).We are not developing a new method, we used an existing one (SPHARM-PDM). However, to be more accurate, we would like to delineate thalamic nuclei on the surface of our meshes (because the nuclei have different functional role). Existing atlases (such as yours) are usable on volumes but not on surfaces. Do you have any idea how we could project your atlas onto a surface? We did not find any method in the scientific literature.
Hope you could help us, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
You can create a surface using mri_binarize listing all the thalamic nuclei with --match and specifying a surface output (you may wan to smooth it a little bit to remove the pixelization). You can then use mri_vol2surf (using the vol2surf in the link below with the --vol2surf option and using the thalamic segmentation itself as the input volume, abs for the projtype and maybe -2 mm for the projdist and interp 0 for nearest). You can then use mris_seg2annot to create an annotation that you can visualize on the surface.
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf
On 6/1/2020 5:33 AM, Quentin Devignes wrote:
External Email - Use Caution
Dear Doctor Iglesias,
Thanks for your previous reply. As agreed, I post my question on the Freesurfer list.
We are doing shape analyses on thalamus in order to determine whether distinct cognitive profiles in Parkinson’s disease have different deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape analysis module in Slicer4) to obtain deformation fields and p-values map (cf. attached file; vectors represent the magnitude of deformation between two groups).We are not developing a new method, we used an existing one (SPHARM-PDM). However, to be more accurate, we would like to delineate thalamic nuclei on the surface of our meshes (because the nuclei have different functional role). Existing atlases (such as yours) are usable on volumes but not on surfaces. Do you have any idea how we could project your atlas onto a surface? We did not find any method in the scientific literature.
Hope you could help us, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
External Email - Use Caution
Dear Doctor Greve,
Thank you for your reply. I am trying to do what you advised me.
For now, I have segmented thalamic nuclei in the left hemisphere, checked and corrected this segmentation and used MRI_binarize as advised. However, I don’t know what to write for the « projmap » option of vol2surf… Could you please help me?
My command line is: vol2surf --vol2surf ***the thalamic segmentation.mgz*** ***the surface obtained from MRI_binarize*** 1 (for projtype option) -2 (for projdist option) X (nothing for projmap option) ‘lta’ (for reg option) ’novsm’ (for vsm option) 0 (for interp option) ***My directory*** (for output option).
Wish you a nice day, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
Le 1 juin 2020 à 16:40, Douglas N. Greve dgreve@mgh.harvard.edu a écrit :
You can create a surface using mri_binarize listing all the thalamic nuclei with --match and specifying a surface output (you may wan to smooth it a little bit to remove the pixelization). You can then use mri_vol2surf (using the vol2surf in the link below with the --vol2surf option and using the thalamic segmentation itself as the input volume, abs for the projtype and maybe -2 mm for the projdist and interp 0 for nearest). You can then use mris_seg2annot to create an annotation that you can visualize on the surface.
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf
On 6/1/2020 5:33 AM, Quentin Devignes wrote:
External Email - Use CautionDear Doctor Iglesias,
Thanks for your previous reply. As agreed, I post my question on the Freesurfer list.
We are doing shape analyses on thalamus in order to determine whether distinct cognitive profiles in Parkinson’s disease have different deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape analysis module in Slicer4) to obtain deformation fields and p-values map (cf. attached file; vectors represent the magnitude of deformation between two groups).We are not developing a new method, we used an existing one (SPHARM-PDM). However, to be more accurate, we would like to delineate thalamic nuclei on the surface of our meshes (because the nuclei have different functional role). Existing atlases (such as yours) are usable on volumes but not on surfaces. Do you have any idea how we could project your atlas onto a surface? We did not find any method in the scientific literature.
Hope you could help us, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
<ShapeComparison_SPHARM-PDM_pMap.png>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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It will ignore the projmap option, so you can just leave it as X (it can be any string, but there does have to be something there). For the reg, use regheader
On 6/4/2020 6:00 AM, Quentin Devignes wrote:
External Email - Use Caution
Dear Doctor Greve,
Thank you for your reply. I am trying to do what you advised me.
For now, I have segmented thalamic nuclei in the left hemisphere, checked and corrected this segmentation and used MRI_binarize as advised. However, I don’t know what to write for the « projmap » option of vol2surf… Could you please help me?
My command line is: vol2surf --vol2surf ***the thalamic segmentation.mgz*** ***the surface obtained from MRI_binarize*** 1 (for projtype option) -2 (for projdist option) X (nothing for projmap option) ‘lta’ (for reg option) ’novsm’ (for vsm option) 0 (for interp option) ***My directory*** (for output option).
Wish you a nice day, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
Le 1 juin 2020 à 16:40, Douglas N. Greve <dgreve@mgh.harvard.edu mailto:dgreve@mgh.harvard.edu> a écrit :
You can create a surface using mri_binarize listing all the thalamic nuclei with --match and specifying a surface output (you may wan to smooth it a little bit to remove the pixelization). You can then use mri_vol2surf (using the vol2surf in the link below with the --vol2surf option and using the thalamic segmentation itself as the input volume, abs for the projtype and maybe -2 mm for the projdist and interp 0 for nearest). You can then use mris_seg2annot to create an annotation that you can visualize on the surface.
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_vol2surf
On 6/1/2020 5:33 AM, Quentin Devignes wrote:
External Email - Use Caution
Dear Doctor Iglesias,
Thanks for your previous reply. As agreed, I post my question on the Freesurfer list.
We are doing shape analyses on thalamus in order to determine whether distinct cognitive profiles in Parkinson’s disease have different deformation fiels of the thalamic surface. We used SPHARM-PDM tool (shape analysis module in Slicer4) to obtain deformation fields and p-values map (cf. attached file; vectors represent the magnitude of deformation between two groups).We are not developing a new method, we used an existing one (SPHARM-PDM). However, to be more accurate, we would like to delineate thalamic nuclei on the surface of our meshes (because the nuclei have different functional role). Existing atlases (such as yours) are usable on volumes but not on surfaces. Do you have any idea how we could project your atlas onto a surface? We did not find any method in the scientific literature.
Hope you could help us, Best regards,
Quentin DEVIGNES PhD candidate in neurosciences Neuropsychologist UMR-S 1172 - Lille Neuroscience and Cognition - FRANCE
<ShapeComparison_SPHARM-PDM_pMap.png>
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Quentin Devignes