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.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.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.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>: >> 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. >> >> _______________________________________________ >> 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! 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