Hi Denis, Indeed the meshes’ vertices are indeed already registered in surface space, i.e. to the fsaverage, and are obtained from the 32k meshes provided in the structural processing package. However, we used wb_command for the subsampling, which as far as I know is in fact doing a re-tessellation on the sphere, rather than selecting a subset of vertices. This means that it’s probably not straightforward to generate an ‘inuse’ vector.
Best, Jan-Mathijs On May 18, 2015, at 4:04 AM, Denis-Alexander Engemann <denis.engem...@gmail.com> wrote: > ... taking a closer look at the reference manual it turns out the dipoles are > already in the standard model space but morphed to individual anatomy, at > least for the 3d models. > I'll take a look at `hcp_anatomy.m` to better understand the details that > would facilitate representing the source models appropriately in MNE data > containers which normally contain a few additional variables (mostly related > to the subsampling of the full freesurfer output) and some meta info. > > Best, > Denis > > > 2015-05-18 2:25 GMT+02:00 Denis-Alexander Engemann <denis.engem...@gmail.com>: > Hi Jan Mathijs, > > the reason was that we're aiming for HCP I/O support in MNE that is as > complete as possible. This means it would be nice to be able to use MNE > functions to create source models which are defined in freesurfer space. > What you suggest might indeed work, I'm giving it a try. That would already > be a start. > But I fear it will not be easy to make some standard MNE routines work with > the shipped source models, , e.g, morphing to fsaverage, etc. This is mainly > because of the coordinate system. But maybe there is a solution to this in > the HCP-MEG pipeline we could learn from? > > As always any hints are welcome. > > Best, > Denis > > > 2015-05-15 22:09 GMT+02:00 jan-mathijs schoffelen <jm.schoffe...@gmail.com>: > Hi Denis, > > Following up on my previous comment: why is it exactly you want the mapping > to freesurfer space? The 123456_meg_anatomy_sourcemodel_2d.mat is already in > helmet space. If you want to use it with MNE suite to create leadfields that > are expressed in the correct coordinate system, I think writing the contents > of the mat-file mentioned to a MNE-suite compatible file with an identity > matrix as the transform. > Or am I missing something? > > Best, > Jan-Mathijs > > > On May 15, 2015, at 3:44 PM, Denis-Alexander Engemann > <denis.engem...@gmail.com> wrote: > >> >> I was wondering wheather the transforms would be suitable for mapping the >> freesurfer surface coordinates to the helmet space. >> If this step would work, the transforms and the coreg would be usable with >> other software such as for example the MNE suite. >> We could then write a routine that skips the regular conversion of BTI files >> and adds identity matrices instead to the related transform fields that >> usually map from BTI to Neuromag space. The transforms provided could then >> be used to map the sensors to the source models created in MNE. >> >> >> Any hint wold be appreciated. >> >> Best, >> Denis >> >> >> >> 2015-05-15 15:35 GMT+02:00 Georgios Michalareas >> <giorgos.michalar...@esi-frankfurt.de>: >> Dear Beth, >> >> the head shape files are not provided with the data. >> The reason for this is that headshape digitization includes points around >> the nose, the eyes, the forehead and the entire head. This means that this >> information could lead to identification of a subjects identity. >> This is also the reason why the structural MR images provided by the MR >> modality have also such external features stripped off the data in order to >> avoid a possible subject identification. >> Following this constraint, in the MEG team we provide both surface(2D) and >> volumetric(3D) source models so that the community can perform source >> localization on them. >> You can find them in the anatomy directory of the released data. >> The surface source model is called >> 177746_MEG_anatomy_sourcemodel_2d.mat >> >> while there are 3 volumetric models with different voxel sizes (4,6,8 mm) >> 177746_MEG_anatomy_sourcemodel_3d4mm.mat >> 177746_MEG_anatomy_sourcemodel_3d6mm.mat >> 177746_MEG_anatomy_sourcemodel_3d8mm.mat >> >> I hope this helps. >> Let me know for anything else. >> Giorgos >> >> >> >> >> On 15/05/2015 15:18, Elizabeth Anne Bock, Ms wrote: >>> I just downloaded the MEG data from the 500 Subjects + MEG2 Data Release. >>> I see from the documentation that the MEG data should include a head shape >>> file. This is not present in my downloaded set. Where can I get these? >>> Thanks, >>> Beth >>> ------------------------------------------------------------------------------------------ >>> >>> Elizabeth Bock / MEG System Engineer >>> >>> McConnell Brain Imaging Centre / Montreal Neurological Institute >>> >>> McGill University / 3801 University St. / Montreal, QC H3A 2B4 >>> >>> >>> >>> MEG Lab: 514.398.6056 >>> >>> Mobile: 514.718.6342 >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> HCP-Users@humanconnectome.org >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> >> >> >> This email is free from viruses and malware because avast! Antivirus >> protection is active. >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> >> >> _______________________________________________ >> HCP-Users mailing list >> HCP-Users@humanconnectome.org >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
