Hi,
I included Eric here who also is an author of PySurfer which we intensely use for visualization. In MNE you subsample the original surfaces to define dipole grids. For subsequent morphing and plotting operations you need to know the slection of original vertices used. If you store a source model, you normally would store all triangles and positions of the original tessalation, the reduced ones, the surface normals, and mapping indices to connect the subsampled locations to the original ones. Also the MNE inverse pipeline rely on the freesurfer coordinate system. To deal with this latter point you would at least need know how to transform the MNE source models to the helmet space ... Best, Denis 2015-05-18 18:42 GMT+02:00 Glasser, Matthew <[email protected]>: > Can someone explain why it is important to use original FreeSurfer > surfaces? These have a much higher density that is needed for most > applications, are very irregular, and do not have vertex correspondence > across subjects. It is possible to resample back to the FreeSurfer native > mesh, but I am puzzled as to why that would be necessary. > > Peace, > > Matt. > > From: Denis-Alexander Engemann <[email protected]> > Date: Monday, May 18, 2015 at 9:35 AM > To: jan-mathijs schoffelen <[email protected]> > Cc: Jair Montoya <[email protected]>, "Elizabeth Anne Bock, Ms" < > [email protected]>, Alexandre Gramfort < > [email protected]>, "[email protected]" < > [email protected]> > Subject: Re: [HCP-Users] where are the head shape file for MEG > > > 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 > > > ------------------------------ > > The materials in this message are private and may contain Protected > Healthcare Information or other information of a sensitive nature. If you > are not the intended recipient, be advised that any unauthorized use, > disclosure, copying or the taking of any action in reliance on the contents > of this information is strictly prohibited. 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