Registration issue
Posted: Mon May 28, 2018 11:37 am
Hello,
I have a non-isotropic volume (t1pre.nii) that I have processed with FreeSurfer.
I have imported the FreeSurfer output back to my BrainVISA database with the "Freesurfer outputs To BrainVisa conversion pipeline".
I want to display the FreeSurfer/MarsAtlas parcellation together with the other volumes I had in my BrainVISA database but I can't understand how to do so with Anatomist.
In the this example I included the original t1pre.nii, together with the freesurfer orig.mgz imported back into the BrainVISA database (freesurfer.nii):
https://www.dropbox.com/s/0ecl6g4wcztxv ... v.zip?dl=0
The two volumes have different voxel sizes but are correctly registered: if I open the two volumes together in MRIcron, BrainSuite, SPM or Brainstorm, they appear correctly aligned. But if I load the two volumes in Anatomist, no matter which referential I select for one or the other volume, I cannot get the linked cursor to point at the same location in the two windows (see screen capture in the .zip file).
How do I get to see the two volumes aligned in Anatomist?
(it's not my primary objective: I have other volumes in my BrainVISA database that I need to display in the same coordinate system as the MarsAtlas parcels computed from the BrainVISA+FreeSurfer pipeline - the issue with the coordinate system is the same for all the volumes and meshes coming from FreeSurfer)
I'm sorry if there is something obvious I'm missing in the way Anatomist handles the transformations between volumes, I'm not very familiar with the software yet.
Thanks for your help
François
I have a non-isotropic volume (t1pre.nii) that I have processed with FreeSurfer.
I have imported the FreeSurfer output back to my BrainVISA database with the "Freesurfer outputs To BrainVisa conversion pipeline".
I want to display the FreeSurfer/MarsAtlas parcellation together with the other volumes I had in my BrainVISA database but I can't understand how to do so with Anatomist.
In the this example I included the original t1pre.nii, together with the freesurfer orig.mgz imported back into the BrainVISA database (freesurfer.nii):
https://www.dropbox.com/s/0ecl6g4wcztxv ... v.zip?dl=0
The two volumes have different voxel sizes but are correctly registered: if I open the two volumes together in MRIcron, BrainSuite, SPM or Brainstorm, they appear correctly aligned. But if I load the two volumes in Anatomist, no matter which referential I select for one or the other volume, I cannot get the linked cursor to point at the same location in the two windows (see screen capture in the .zip file).
How do I get to see the two volumes aligned in Anatomist?
(it's not my primary objective: I have other volumes in my BrainVISA database that I need to display in the same coordinate system as the MarsAtlas parcels computed from the BrainVISA+FreeSurfer pipeline - the issue with the coordinate system is the same for all the volumes and meshes coming from FreeSurfer)
I'm sorry if there is something obvious I'm missing in the way Anatomist handles the transformations between volumes, I'm not very familiar with the software yet.
Thanks for your help
François