Re: [HCP-Users] where are the head shape file for MEG
Hi Georgios, I am trying to work with the transformations provided in the anatomy directory, as you mentioned, below. I understand the the fiducials are in 'vox' space, and I assume they are in the 1mm vox space. The anatomy file provided, however is in 0.7mm vox space. How do I get the fiducials in the 0.7mm vox space since I do not see a vox2vox transform? 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 From: Georgios Michalareas [giorgos.michalar...@esi-frankfurt.de] Sent: Friday, May 15, 2015 10:47 AM To: Elizabeth Anne Bock, Ms; Denis-Alexander Engemann Cc: hcp-users@humanconnectome.org; Jair Montoya; Alexandre Gramfort; Francois Tadel Subject: Re: [HCP-Users] where are the head shape file for MEG I am not sure I fully understood what you would like to do in MNE and Brainstorm bur maybe the following are of help : In the anatomy directory there is an ascii file 177746_MEG_anatomy_transform.txt containing the structure variable transform, which contains a big list of transformation matrices contained in fields: vox2bti: [4x4 double] bti2vox: [4x4 double] vox2spm: [4x4 double] spm2vox: [4x4 double] spm2bti: [4x4 double] bti2spm: [4x4 double] The 2D and 3D source models I mentioned in my earlier email (see below) are defined on the HEAD coordinate system (nasion, left and right peri-auricular points (NAS, LPA and RPA, respectively)). This means you dont need to apply any transform on them in order to perform source analysis wth the MEG data. Now if you want to transform the source models to MNI ( anterior / posterior commissural line) space you can apply to the source model positions the bti2spm transformation matrix. If you want to use the fiducial and landmark locations you can use the files from the anatomy directory 177746_MEG_anatomy_fiducials.txt (NAS, LPA and RPA,) 177746_MEG_anatomy_landmarks.txt (AC, PC) The positions of the fiducials there are defined on a voxel space which you do not hae accesss to. (An MR with full facial features). So to use them you need to first apply to their voxel coordinates the vox2bti for HEAD space or vox2spm for MNI space. I hope this helps Best Giorgos On 15/05/2015 15:54, Elizabeth Anne Bock, Ms wrote: We would like to use the HCP data in brainstorm. Ideally we would like to use the head-shape file and/or coil coordinates to generate a transform - but I understand the restrictions. What you suggest could be a viable solution - having the transforms and coreg would be very helpful. 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 From: Denis-Alexander Engemann [denis.engem...@gmail.commailto:denis.engem...@gmail.com] Sent: Friday, May 15, 2015 9:44 AM To: Georgios Michalareas Cc: Elizabeth Anne Bock, Ms; hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org; Jair Montoya; Alexandre Gramfort Subject: Re: [HCP-Users] where are the head shape file for MEG 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.demailto: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
Re: [HCP-Users] where are the head shape file for MEG
Thanks, Jan-Mathijs. It isn't so much that we need the location of the fiducials, but more that we need to be able to do the co-registration. Since we do not have the headshape file, I was under the impression that we could use the fiducials provided and the transformations to get the fiducial points onto the MRI. Mostly because we would like to offer Brainstorm users an analysis pipeline and therefore we require the users to confirm accurate co-registration. If I would like to compute my own source models and I cannot use the fiducials and the transformations, maybe you can suggest how I can do the co-registration on the raw data. 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 From: jan-mathijs schoffelen [jm.schoffe...@gmail.com] Sent: Friday, June 19, 2015 1:44 PM To: Elizabeth Anne Bock, Ms Cc: Georgios Michalareas; Denis-Alexander Engemann; Jair Montoya; hcp-users@humanconnectome.org; Alexandre Gramfort; Francois Tadel Subject: Re: [HCP-Users] where are the head shape file for MEG Hi Beth, Allow me to chime in here: I would discourage you to rely on the fiducial and landmark locations as provided. These I have clicked in the 1mm anaromical images at their rough locations, so they are not very accurate (and I use them for an initial coregistration). Even if you had the 1 mm image available, they are pretty useless. (by the way, the vox2vox transform can be obtained by an appropriate combination of the vox2bti and vox07mm2bti, I would guess that vox2vox07mm = vox07mm2bti\vox2bti in MATLAB terminology, or equivalently bti2vox07mm*vox2bti) It sounds between the lines that Brainstorm needs the location of the fiducials? If their exact location on the X/Y/Z-axes is not too crucial I would do an inverse warp (with the bti2vox07mm transformation matrix of a few ‘well chosen’ points on the X and Y-axes (e.g. (60,0,0), (0,-60,0) and (0,60,0) for the NAS,RPA and LPA, respectively). Best, Jan-Mathijs On Jun 19, 2015, at 7:01 PM, Elizabeth Anne Bock, Ms elizabeth.b...@mcgill.camailto:elizabeth.b...@mcgill.ca wrote: Hi Georgios, I am trying to work with the transformations provided in the anatomy directory, as you mentioned, below. I understand the the fiducials are in 'vox' space, and I assume they are in the 1mm vox space. The anatomy file provided, however is in 0.7mm vox space. How do I get the fiducials in the 0.7mm vox space since I do not see a vox2vox transform? 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 From: Georgios Michalareas [giorgos.michalar...@esi-frankfurt.demailto:giorgos.michalar...@esi-frankfurt.de] Sent: Friday, May 15, 2015 10:47 AM To: Elizabeth Anne Bock, Ms; Denis-Alexander Engemann Cc: hcp-users@humanconnectome.orgmailto:hcp-users@humanconnectome.org; Jair Montoya; Alexandre Gramfort; Francois Tadel Subject: Re: [HCP-Users] where are the head shape file for MEG I am not sure I fully understood what you would like to do in MNE and Brainstorm bur maybe the following are of help : In the anatomy directory there is an ascii file 177746_MEG_anatomy_transform.txt containing the structure variable transform, which contains a big list of transformation matrices contained in fields: vox2bti: [4x4 double] bti2vox: [4x4 double] vox2spm: [4x4 double] spm2vox: [4x4 double] spm2bti: [4x4 double] bti2spm: [4x4 double] The 2D and 3D source models I mentioned in my earlier email (see below) are defined on the HEAD coordinate system (nasion, left and right peri-auricular points (NAS, LPA and RPA, respectively)). This means you dont need to apply any transform on them in order to perform source analysis wth the MEG data. Now if you want to transform the source models to MNI ( anterior / posterior commissural line) space you can apply to the source model positions the bti2spm transformation matrix. If you want to use the fiducial and landmark locations you can use the files from the anatomy directory 177746_MEG_anatomy_fiducials.txt (NAS, LPA and RPA,) 177746_MEG_anatomy_landmarks.txt (AC, PC) The positions of the fiducials there are defined on a voxel space which you do not hae accesss to. (An MR with full facial features). So to use them you need to first apply to their voxel coordinates the vox2bti for HEAD space or vox2spm for MNI space. I hope
Re: [HCP-Users] where are the head shape file for MEG
If you are talking about resampling the low-resolution data onto the higher resolution mesh, yes, you can resample either direction (uses the same files, in fact, just reverse them). You will need the spheres used to downsample the surface in the first place. Look at http://www.humanconnectome.org/software/workbench-command.php?function=-metric-resample (and maybe also -label-resample and -surface-resample). Tim On Mon, May 18, 2015 at 9:18 PM, Denis-Alexander Engemann denis.engem...@gmail.com wrote: 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 tsc...@mst.edu: 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
Re: [HCP-Users] where are the head shape file for MEG
Generally I thought you could only directly subsample the regular icosahedron spheres (e.g. 2562, 10242, 40962, 163492). The native mesh sphere isn’t going to be amenable to that sort of thing as it is very irregular (varying numbers of neighbors per vertex, varying vertex spacing, etc). One can certainly resample from one spherical mesh to another (this is how we get MRI data onto a standard mesh were vertices have correspondence across subjects). Additionally, one can resample an anatomical surface from one mesh to another. When this is done, the surface remains in the same volume space (could be native volume space, MNI volume space, FreeSurfer coordinate space, even “helmet space” if that is not the same as one of the previous 3 spaces). I’m guessing that there is not any theoretical reason why any of the MEG software cannot use standard meshes, but perhaps there are implementation issues. Peace, Matt. From: Denis-Alexander Engemann denis.engem...@gmail.com Date: Monday, May 18, 2015 at 11:56 AM To: Matt Glasser glass...@wusm.wustl.edu Cc: jan-mathijs schoffelen jm.schoffe...@gmail.com, Jair Montoya montoya.j...@gmail.com, Elizabeth Anne Bock, Ms elizabeth.b...@mcgill.ca, Alexandre Gramfort alexandre.gramf...@gmail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org, Eric Larson larson.eri...@gmail.com Subject: Re: [HCP-Users] where are the head shape file for MEG 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 GMT02:00 Glasser, Matthew glass...@wusm.wustl.edu: 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 denis.engem...@gmail.com Date: Monday, May 18, 2015 at 9:35 AM To: jan-mathijs schoffelen jm.schoffe...@gmail.com Cc: Jair Montoya montoya.j...@gmail.com, Elizabeth Anne Bock, Ms elizabeth.b...@mcgill.ca, Alexandre Gramfort alexandre.gramf...@gmail.com, hcp-users@humanconnectome.org hcp-users@humanconnectome.org 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 GMT02:00 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 GMT02:00 Denis-Alexander Engemann denis.engem...@gmail.com: Hi Jan Mathijs, the reason was that we're aiming for HCP I/O support in MNE
Re: [HCP-Users] where are the head shape file for MEG
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
Re: [HCP-Users] where are the head shape file for MEG
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
Re: [HCP-Users] where are the head shape file for MEG
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
Re: [HCP-Users] where are the head shape file for MEG
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. http://www.avast.com ___ HCP-Users mailing list HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users
Re: [HCP-Users] where are the head shape file for MEG
We would like to use the HCP data in brainstorm. Ideally we would like to use the head-shape file and/or coil coordinates to generate a transform - but I understand the restrictions. What you suggest could be a viable solution - having the transforms and coreg would be very helpful. 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 From: Denis-Alexander Engemann [denis.engem...@gmail.com] Sent: Friday, May 15, 2015 9:44 AM To: Georgios Michalareas Cc: Elizabeth Anne Bock, Ms; hcp-users@humanconnectome.org; Jair Montoya; Alexandre Gramfort Subject: Re: [HCP-Users] where are the head shape file for MEG 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.demailto: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.orgmailto:HCP-Users@humanconnectome.org http://lists.humanconnectome.org/mailman/listinfo/hcp-users [http://static.avast.com/emails/avast-mail-stamp.png] http://www.avast.com/ This email is free from viruses and malware because avast! Antivirushttp://www.avast.com/ protection is active. ___ HCP-Users mailing list HCP-Users@humanconnectome.orgmailto: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
Re: [HCP-Users] where are the head shape file for MEG
I am not sure I fully understood what you would like to do in MNE and Brainstorm bur maybe the following are of help : In the anatomy directory there is an ascii file 177746_MEG_anatomy_transform.txt containing the structure variable transform, which contains a big list of transformation matrices contained in fields: vox2bti: [4x4 double] bti2vox: [4x4 double] vox2spm: [4x4 double] spm2vox: [4x4 double] spm2bti: [4x4 double] bti2spm: [4x4 double] The 2D and 3D source models I mentioned in my earlier email (see below) are defined on the HEAD coordinate system (nasion, left and right peri-auricular points (NAS, LPA and RPA, respectively)). This means you dont need to apply any transform on them in order to perform source analysis wth the MEG data. Now if you want to transform the source models to MNI (anterior / posterior commissural line) space you can apply to the source model positions the bti2spm transformation matrix. If you want to use the fiducial and landmark locations you can use the files from the anatomy directory 177746_MEG_anatomy_fiducials.txt (NAS, LPA and RPA,) 177746_MEG_anatomy_landmarks.txt (AC, PC) The positions of the fiducials there are defined on a voxel space which you do not hae accesss to. (An MR with full facial features). So to use them you need to first apply to their voxel coordinates the vox2bti for HEAD space or vox2spm for MNI space. I hope this helps Best Giorgos On 15/05/2015 15:54, Elizabeth Anne Bock, Ms wrote: We would like to use the HCP data in brainstorm. Ideally we would like to use the head-shape file and/or coil coordinates to generate a transform - but I understand the restrictions. What you suggest could be a viable solution - having the transforms and coreg would be very helpful. 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 *From:* Denis-Alexander Engemann [denis.engem...@gmail.com] *Sent:* Friday, May 15, 2015 9:44 AM *To:* Georgios Michalareas *Cc:* Elizabeth Anne Bock, Ms; hcp-users@humanconnectome.org; Jair Montoya; Alexandre Gramfort *Subject:* Re: [HCP-Users] where are the head shape file for MEG 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 mailto: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
