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<mailto:denis.engem...@gmail.com>]
Sent: Friday, May 15, 2015 9:44 AM
To: Georgios Michalareas
Cc: Elizabeth Anne Bock, Ms;
hcp-users@humanconnectome.org<mailto: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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