Hi Beth, It is not clear in concreto what you mean with the particulars of the ‘coregistration’ that Brainstorm uses. If you want to compute your own source model from the anatomical that is released (i.e. the 0.7 mm T1 images), the only coregistration information that you need is provided by transform.vox7mm2bti. If you want to compute your own source model and start from the cortical sheets that have been provided in the Structural Preprocessing package, the coregistration information that you need is provided by transform.spm2bti. In other words, although you shouldn’t rely on the released fiducial locations, the transformation matrices are accurate and contain the coregistration information that you need. If it’s about the users confirming the co-registration, I guess you would want to show them in the GUI an image of a head surface (not provided by HCP, but reconstructable in probably a relatively poor quality due to defacing and FOV-issues) with some dummy fiducials projected onto them? My suggestion would be to use as ‘fiducials’ the locations where the X and Y-axes cut through the head surface. The best thing of course would be to just use the source model and volume conduction model that has been constructed and provided by the consortium.
Best, Jan-Mathijs On Jun 19, 2015, at 9:56 PM, Elizabeth Anne Bock, Ms <[email protected]> wrote: > 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 [[email protected]] > Sent: Friday, June 19, 2015 1:44 PM > To: Elizabeth Anne Bock, Ms > Cc: Georgios Michalareas; Denis-Alexander Engemann; Jair Montoya; > [email protected]; 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 > <[email protected]> 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 [[email protected]] >> Sent: Friday, May 15, 2015 10:47 AM >> To: Elizabeth Anne Bock, Ms; Denis-Alexander Engemann >> Cc: [email protected]; 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 [[email protected]] >>> Sent: Friday, May 15, 2015 9:44 AM >>> To: Georgios Michalareas >>> Cc: Elizabeth Anne Bock, Ms; [email protected]; 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<[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 >>> >>> >>> >>> >>> This email is free from viruses and malware because avast! Antivirus >>> protection is active. >>> >>> _______________________________________________ >>> HCP-Users mailing list >>> [email protected] >>> http://lists.humanconnectome.org/mailman/listinfo/hcp-users >>> >> >> >> >> >> This email is free from viruses and malware because avast! 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