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. / Montreal, QC H3A 2B4
MEG Lab: 514.398.6056
Mobile: 514.718.6342
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