Thanks Tim, just a simple question. Would it then be possible re-map the resampled topologies to the original ones or not? If it is possible, how could it be achieved?
Cheers, Denis 2015-05-19 0:57 GMT+02:00 Timothy Coalson <[email protected]>: > 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 < > [email protected]> 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 <[email protected] >> >: >> >>> 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 < >>> [email protected]> 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 < >>> [email protected]>: >>> >>>> 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 < >>>> [email protected]>: >>>> >>>>> 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 < >>>>> [email protected]> 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 < >>>>> [email protected]>: >>>>> >>>>>> 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 >>>>>> [email protected] >>>>>> 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 >>>>>> [email protected] >>>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>>> >>>>> >>>>> _______________________________________________ >>>>> HCP-Users mailing list >>>>> [email protected] >>>>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>>>> >>>>> >>>>> >>>> >>> >>> >> _______________________________________________ >> HCP-Users mailing list >> [email protected] >> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >> > > _______________________________________________ HCP-Users mailing list [email protected] http://lists.humanconnectome.org/mailman/listinfo/hcp-users
