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 <dgr...@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 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> >> >> >> >> _______________________________________________ >> 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> > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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