Back on this other question, wb_command indeed does not do decimation of the "remove vertices from existing topology" variety. The usual way to do surface downsampling with wb_command is to generate a new sphere with the desired number of vertices (and highly regular topology/spacing), and then resample data and anatomical surfaces to it from the current sphere (which uses a set of weights at each vertex, computed from the location and topology of sphere vertices).
As such, the mapping between vertices on old and new topologies is many-to-many, with real-valued weights. Tim On Mon, May 18, 2015 at 9:35 AM, Denis-Alexander Engemann < denis.engem...@gmail.com> wrote: > > 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. > > > Arff. My prediction is that computing solutions will ultimately work, all > plotting will be severly broken as this involves the original freesurfer > surfaces. It would be good to have a mapping between the resampled vertices > and the original vertices if this is possible at all (?). > Any chances we can trigger some workaround / action to get the trafos > between bti and freesurfer? This would facilitate many things and would > allow for a more complete bridge between the HCP MEG data and different > software environments. > Where would you start? > > Best, > Denis > > > 2015-05-18 7:30 GMT+02:00 jan-mathijs schoffelen <jm.schoffe...@gmail.com> > : > >> 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 >>>>> >>>>> >>>>> >>>>> >>>>> ------------------------------ >>>>> <http://www.avast.com/> >>>>> >>>>> This email is free from viruses and malware because avast! Antivirus >>>>> <http://www.avast.com/> 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 > _______________________________________________ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
