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 <dgr...@mgh.harvard.edu
<mailto: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
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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