Index of "datafiles"
The following files contain detailed information about the data files used for our human
skull analyses.All files but jack*.bin are MATLAB archive files, so they can be readily
opened using the load <filename.bin> -mat command at the Matlab prompt.
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Attention NETSCAPE Users
You must right-click on a filename and then choose "Save Link As"
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Name Last modified Size (Description below)
![[ ]](images/largebut.gif)
surface_data.bin 25-Mar-98 16:07 3.0M
mesh_data.bin 10-Apr-98 15:10 215k
mesh_data_old.bin 26-Mar-98 15:27 162k
CT_PCS_trans.bin 26-Mar-98 15:26 6k
forward_BEM.bin 25-Mar-98 16:05 4.8M
forward_2sph.bin 25-Mar-98 16:04 16.8M
true_loc_ori.bin 25-Mar-98 16:07 3k
phantom_eeg_meg.bin 26-Mar-98 15:33 13.3M
jack_256x256x325.bin 15-May-98 10:01 20.3M
jack_256x256x325.bin.gz 15-May-98 10:02 9.7M
Mingxiong Huang, Ph.D. 3/24/98
Updates:
Sylvain Baillet, Ph.D. 3/14/00 - Fixed some downloading problems when using NetScape
The following list contains the names of the files and the description
of the individual variables (.bin extensions are replaced by .mat when dealing
with a Matlab archive file - sorry for the inconvenience)
1) surface_data.mat: raw surface data files in CT coordinate system.
scalp (210983 x 3) x,y,z of those points that for scalp.
skull (186406 x 3) x,y,z of those points that for skull.
brain (125359 x 3) x,y,z of those points that for brain.
2) mesh_data.mat: tessellated surface data in both CT and patient coordinate
system (PCS). The meshes in PCS system are in meters.
mesh_scalp_ct (1148 x 3) x,y,z of triangular mesh nodes for scalp
in CT system.
mesh_skull_ct (1148 x 3) x,y,z of triangular mesh nodes for skull
in CT system.
mesh_brain_ct (1148 x 3) x,y,z of triangular mesh nodes for brain
in CT system.
mesh_scalp (1148 x 3) x,y,z of triangular mesh nodes for scalp
in PCS system.
mesh_skull (1148 x 3) x,y,z of triangular mesh nodes for skull
in PCS system.
mesh_brain (1148 x 3) x,y,z of triangular mesh nodes for brain
in PCS system.
geo (3 x 2292) relation matrix containing the node
index for each triangles.
3) CT_PCS_trans.mat: this file contains the information that one need to
transform a point (or points) from CT coordinate to PCS. We used the
electrodes identified from CT slices and those measured in patient coordinate
system to form the transformation. Since dipole #59 is outside the FOV of the
CT scans, it was not included in the calculation. If A_CT is a 3 by M location
matrix in CT system, to transform A_CT into PCS to form A_PCS (also M by 3),
one can use:
>> A_PCS = scale_ct2pcs*Q_ct2pcs' * (A_CT-CT_cen*ones(1,M)) + ...
PCS_cen*ones(1,M);
One the other hand, to transform from PCS into CT system, one can use:
>> A_CT = scale_pcs2ct*Q_pcs2ct' * (A_PCS-PCS_cen*ones(1,M)) + ...
CT_cen*ones(1,M);
eeg_ct_all (64 x 4) the 1st column is the EEG electrode index.
Dipole #59 is excluded. The rest 3 columns are the
coordinates in the CT system.
eeg_pcs (65 x 3) x,y,z coordinates of the 65 EEG electrodes
measured in PCS in mm.
eeg_ct2pcs (65 x 3) x,y,z coordinates of the 65 EEG electrodes
identified from CT and transformed to PCS in mm.
CT_cen, PCS_cen, Q_ct2pcs, Q_pcs2ct, scale_ct2pcs, scale_pcs2ct are
variables used in the transformations.
4) forward_BEM.mat: forward calculation of MEG and EEG for a dipole grid
using BEM model. For the MEG, 4 out of 122 channels were bad channels, hence,
the gain was calculated for the 118 good channels.
gain_grid_BEM_eeg (64 x 3444) gain matrix for EEG BEM.
gain_grid_BEM_meg (118 x 3444) gain matrix for MEG BEM.
grid_dip_BEM (1148 x 3) x,y,z of dipole grid for BEM in PCS.
5) forward_2sph.mat: forward calculation of MEG and EEG for a dipole grid
using 2-locally fitted spherical model.
center1 (1 x 1) best fitting center for left-center area.
center2 (1 x 1) best fitting center for left-occipital area.
conduct (1 x 3) conductivities for scalp, skull, brain.
radius_sph1 (1 x 3) radius of 3-concentric spheres for left-
center area.
radius_sph2 (1 x 3) the radius of 3-concentric spheres for left-
occipital area.
dip_cen_id (32 x 1) indicate which spherical center for which
dipole. For example, "dip_cen_id(1) = 1" means
"center1" should be used for dipole #1.
eeg_pcs_center1 (65 x 3) the 65 EEG electrodes mapped to the spherical
scalp with "center1" as the center. The 65th electrode
is the reference electrode.
eeg_pcs_center2 (65 x 3) the 65 EEG electrodes mapped to the spherical
scalp with "center2" as the center. The 65th electrode
is the reference electrode.
grid_dip_centered (2016 x 3) x,y,z of dipole grid for 2-locally
fitted spherical model.
gain_grid_2sph_eeg1 (64 x 6048) EEG gain matrix using "center1"
gain_grid_2sph_eeg2 (64 x 6048) EEG gain matrix using "center2"
gain_grid_2sph_meg1 (118 x 6048) MEG gain matrix using "center1"
gain_grid_2sph_meg2 (118 x 6048) MEG gain matrix using "center2"
6) true_loc_ori.mat: true locations and orientations of dipoles.
dip_loc_ct_true (32 x 3) true dipole locations in CT system.
dip_ori_ct_true (32 x 3) true dipole orientations in CT system.
dip_loc_pcs_true (32 x 3) true dipole locations in PCS system.
dip_ori_pcs_true (32 x 3) true dipole orientations in PCS.
7) phantom_eeg_meg.mat: contains the EEG and MEG data for the human skull
phantom.
eeg_pcs (65 x 3) EEG electrode locations in x,y,z. The first 64
rows are for the 64 measurement electrodes. The last
one is the reference electrode.
eeg_ct2pcs (65 x 3) EEG electrode locations in x,y,z. The first 64
rows are for the 64 electrodes identified from CT and
transformed into PCS. The last one is the reference
electrode.
R (118 x 6) MEG sensor locations in x,y,z. The original
MEG data were collected using Neuromag 122 with 122
planar gradiometers. Four bad channels were deleted.
Each of the remaining 188 channels contains two
pick-up coils. So, the first 3 columns are for the
first coils, and the next 3 columns for the second
coils.
O (118 x 6) corresponding MEG sensor orientations.
EEG_latency1, EEG_latency2, ..., EEG_latency32 (1 x 176): the EEG time
latencies for dipole 1, 2, ..., 32.
EEGwf1, EEGwf2, ..., EEGwf32 (64 x 176): EEG waveforms for dipole 1,
2,...,32. Each row is for one EEG channel.
MEG_latency1, MEG_latency2, ..., MEG_latency32 (1 x 351): the MEG time
latencies for dipole 1, 2, ..., 32.
MEGwf1, MEGwf2, ..., MEGwf32 (118 x3516): MEG waveforms for dipole 1,
2,...,32. Each row is for one MEG channel.
8) jack_256x256x325.bin: contains the raw CT data, from isotropically
resampled CT scans.
This file contains a stack of 325 coronal sections
of the phantom with a maximum gray level of 255
and resolution of 256x256.
The voxel size is 0.58x0.58x0.58 (mm^3).
The file is in binary format and each voxel is
stored as a single byte.
The following pseudo-code can be used to load
and process the image slice by slice:
File_Handle = FOPEN('jack_256x256x325.bin','BINARY_MODE')
FOR K = 1 TO 325
FSEEK(File_Handle, k*256*256, SEEK_FIRST)
Image = FREAD(File_Handle, 256*256, 'UCHAR')
.... process(Image) ....
NEXT K
9) jack_256x256x325.bin.gz: Contains GNU zipped (compressed) raw CT data,
from isotropically resampled CT scans.
Downloading this file may reduce the download time
by half but you must use the UNIX program "gunzip"
to restore the file.
