Hello,
I am following the cook book in order to create head models and find the lead field matrix. I have just finished using mne_prepare_model_bem. How do I view my results and how do I prepare this output for mne_do_forward_solution so that I can find the lead field matrix?
Isaiah Smith
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Hi Isaiah,
It may be helpful to start with the sample data set chapter (and run
through that example). This will take you step by step through the
basic analysis procedure and show you how to perform each of the
checks etc.
HTH,
D
Hello D,
I went through the tutorial and I am wondering how I can find the lead field matrix and create source models from my data in MATLAB after having made the volume conduction models.
Isaiah
Hi Isaiah,
I'm not really sure from your email what you are having difficulty
with. In "The sample data set" chapter
(http://martinos.org/mne/stable/manual/sampledata.html), there is a
description of how to perform these steps in the following
subsections:
The forward solution
The inverse operator decomposition
Interactive analysis
If there is a particular part of this you are having trouble with, can
you describe the problem you are having in more detail.
HTH,
D
Hello D,
What I am trying to say is that I did the tutorial, and I am now trying to do it with other data that I have. I have a file containing the location of the electrodes in a .elc format and I am wondering how to incorporate these electrodes onto my head model. In addition, where can I find the file containing the lead field matrix? Just the matrix.
Isaiah
Hello D,
What I am trying to say is that I did the tutorial, and I am now trying to do it with other data that I have. I have a file containing the location of the electrodes in a .elc format and I am wondering how to incorporate these electrodes onto my head model.
I'm not familiar with the .elc format. Were you able to convert the
raw EEG file to fiff format? There may be a tool for doing this
automatically, in the file conversion. Can you tell me more about your
data? What system it was generated by? If you converted the raw EEG
data? What tool you used to convert the data?
If there isn't a tool you can always manipulate the raw fif file in
MATLAB and add in the necessary fields to your raw file and save it to
a new file (but first let's find out if there is an automated tool).
In addition, where can I find the file containing the lead field matrix? Just the matrix.
The lead field matrix is in the -fwd.fif file you created in the
sample tutorial. The MNE matlab toolbox has a function (the manual
chapter describes how to read it and what the different fields are) if
i remember correctly, it is mne_read_forward_solution(<fname>)).
HTH,
D
Hello D,
A lab in Taiwan sent MRI data to the lab that I am working in to make the head models using the patients? images.
[cid:69575775-A7D6-4576-A1CB-76B7479DB18F at host.ucla.edu]
Using MRICron, I converted the images into .nii, and then using freesurfer get the T1.mgz, which I then use throughout the MNE process.
In addition to the MRIs that we were given, the lab also sent us some the locations of the electrodes in the .elc file . This file can be opened in MATLAB and made into a MATLAB file.
[cid:DA3097A6-4A86-4B04-8BAC-25EF0D240CC9 at host.ucla.edu]
Contents
GEOMETRY START # Do not edit!
HELMET_SYSTEM = 0
PLANAR_SENSORS = 0
SENSOR_SHAPE = 0
SENSOR_ORDER = 0
SENSOR_DIAMETER_X_MM = 10
SENSOR_DIAMETER_Y_MM = 10
SYSTEM_CENTER_X_MM = 1000000000#
SYSTEM_CENTER_Y_MM = 1000000000#
SYSTEM_CENTER_Z_MM = 1000000000#
BASELENGTH_MM = -1
GEOMETRY END
SENSORS START # Do not edit!
LIST_DESCRIPTION = SENSORS
LIST_UNITS = mm
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 3
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 1
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
SENSORS END
SENSORS START_LIST # Do not edit!
24.5 -107.6 69.1
-8.3 -112 69.1
-38.4 -102.2 68.6
74.2 -63.3 57.6
46.9 -62.6 112.7
-4.7 -70.2 130.3
-56.2 -58.9 114.4
-83.2 -59.5 61.4
76.2 -35.3 89.7
28.2 -33.2 140.7
-37.8 -32.8 141.4
-86.7 -32.8 92.3
77.1 24.5 -8.5
87.6 -4.2 48
61.3 -0.6 126.5
-5.2 -2.2 154.7
-72.9 2.3 124.5
-97.5 2.9 50.6
-86.6 26.4 -5.4
76.8 28 85.2
28.7 35.6 139.1
-37 35.7 140.6
-87.2 34 86.2
68.1 52.3 46.6
46.9 59.7 103.6
-5.5 65.8 120
-56.1 62.4 100.4
-79.2 58.1 46.3
-3.7 82.5 88.1
24.8 85.9 50.7
-4.1 91.6 52
-30.1 89.4 47.9
55.3 -85.8 65.1
33.8 -86.9 98.1
-45 -84.4 96.4
-65 -82.1 66.3
63.3 -63.1 86.3
25.5 -64.9 124
-35.4 -64.4 126.3
-71.4 -61.2 90.1
56.3 -30.9 120.6
-4.3 -37.7 148.3
-64.4 -32.1 121.8
82.4 -3.4 88
29.8 1.9 146.1
-38.2 0.2 145.8
-91.2 -0.1 88.6
60 34.3 117.4
-4.5 36 144.6
-68.6 35.4 119.1
63.8 54.5 74.8
25 61.3 117.2
-32.1 63.9 115.9
-71.2 61.3 74.8
47.3 72.4 67.3
35.8 75 85.7
-43.8 78.8 83.4
-55.5 78.6 65.1
84.1 -35.9 51.8
-93.5 -28.4 55.1
82 25.9 44.1
-90 31.2 44.5
48.9 73.7 47.8
-55.1 79.8 45.1
SENSORS END_LIST
NUMBERS START # Do not edit!
LIST_DESCRIPTION = SensorNumbers
LIST_UNITS =
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 1
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 0
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
NUMBERS END
NUMBERS START_LIST # Do not edit!
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
NUMBERS END_LIST
LABELS START # Do not edit!
LIST_DESCRIPTION = SensorLabels
LIST_UNITS =
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 40
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 5
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
LABELS END
LABELS START_LIST # Do not edit!
FP1
FPZ
FP2
F7
F3
FZ
F4
F8
FC5
FC1
FC2
FC6
M1
T7
C3
CZ
C4
T8
M2
CP5
CP1
CP2
CP6
P7
P3
PZ
P4
P8
POZ
O1
OZ
O2
AF7
AF3
AF4
AF8
F5
F1
F2
F6
FC3
FCZ
FC4
C5
C1
C2
C6
CP3
CPZ
CP4
P5
P1
P2
P6
PO5
PO3
PO4
PO6
FT7
FT8
TP7
TP8
PO7
PO8
Labels END_LIST
Can this in MATLAB be converted to .fiff?
The EEG Data is given in the formats shown below. We have not been able to convert the data. But we know that it can be converted to MATLAB through FieldTrip.
[cid:DBC802A4-C669-4401-B187-5E2E953C5E80 at host.ucla.edu]
Thank you,
Isaiah
Hi Isaiah,
Can you contact the lab (or track it down yourself) and find out what
format the data are in? What machine the data were collected with etc.? It
is very hard to help without these specific details.
D
PS
You should be able to convert the mri files directly with mri_convert
(without using MRICRON).
Hello D,
A lab in Taiwan sent MRI data to the lab that I am working in to make the
head models using the patients? images.
Using MRICron, I converted the images into .nii, and then using
freesurfer get the T1.mgz, which I then use throughout the MNE process.
In addition to the MRIs that we were given, the lab also sent us some the
locations of the electrodes in the .elc file . This file can be opened in
MATLAB and made into a MATLAB file.Contents
GEOMETRY START # Do not edit!
HELMET_SYSTEM = 0
PLANAR_SENSORS = 0
SENSOR_SHAPE = 0
SENSOR_ORDER = 0
SENSOR_DIAMETER_X_MM = 10
SENSOR_DIAMETER_Y_MM = 10
SYSTEM_CENTER_X_MM = 1000000000#
SYSTEM_CENTER_Y_MM = 1000000000#
SYSTEM_CENTER_Z_MM = 1000000000#
BASELENGTH_MM = -1
GEOMETRY ENDSENSORS START # Do not edit!
LIST_DESCRIPTION = SENSORS
LIST_UNITS = mm
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 3
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 1
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
SENSORS ENDSENSORS START_LIST # Do not edit!
24.5 -107.6 69.1
-8.3 -112 69.1
-38.4 -102.2 68.6
74.2 -63.3 57.6
46.9 -62.6 112.7
-4.7 -70.2 130.3
-56.2 -58.9 114.4
-83.2 -59.5 61.4
76.2 -35.3 89.7
28.2 -33.2 140.7
-37.8 -32.8 141.4
-86.7 -32.8 92.3
77.1 24.5 -8.5
87.6 -4.2 48
61.3 -0.6 126.5
-5.2 -2.2 154.7
-72.9 2.3 124.5
-97.5 2.9 50.6
-86.6 26.4 -5.4
76.8 28 85.2
28.7 35.6 139.1
-37 35.7 140.6
-87.2 34 86.2
68.1 52.3 46.6
46.9 59.7 103.6
-5.5 65.8 120
-56.1 62.4 100.4
-79.2 58.1 46.3
-3.7 82.5 88.1
24.8 85.9 50.7
-4.1 91.6 52
-30.1 89.4 47.9
55.3 -85.8 65.1
33.8 -86.9 98.1
-45 -84.4 96.4
-65 -82.1 66.3
63.3 -63.1 86.3
25.5 -64.9 124
-35.4 -64.4 126.3
-71.4 -61.2 90.1
56.3 -30.9 120.6
-4.3 -37.7 148.3
-64.4 -32.1 121.8
82.4 -3.4 88
29.8 1.9 146.1
-38.2 0.2 145.8
-91.2 -0.1 88.6
60 34.3 117.4
-4.5 36 144.6
-68.6 35.4 119.1
63.8 54.5 74.8
25 61.3 117.2
-32.1 63.9 115.9
-71.2 61.3 74.8
47.3 72.4 67.3
35.8 75 85.7
-43.8 78.8 83.4
-55.5 78.6 65.1
84.1 -35.9 51.8
-93.5 -28.4 55.1
82 25.9 44.1
-90 31.2 44.5
48.9 73.7 47.8
-55.1 79.8 45.1
SENSORS END_LISTNUMBERS START # Do not edit!
LIST_DESCRIPTION = SensorNumbers
LIST_UNITS =
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 1
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 0
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
NUMBERS ENDNUMBERS START_LIST # Do not edit!
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
NUMBERS END_LISTLABELS START # Do not edit!
LIST_DESCRIPTION = SensorLabels
LIST_UNITS =
LIST_NR_ROWS = 64
LIST_NR_COLUMNS = 40
LIST_NR_TIMEPTS = 1
LIST_VALID = 1
LIST_BINARY = 0
LIST_TYPE = 5
LIST_TRAFO_TYPE = 0
LIST_FIRST_COLUMN = 1
LIST_INDEX_MIN = -1
LIST_INDEX_MAX = -1
LIST_INDEX_ABS_MAX = -1
LABELS ENDLABELS START_LIST # Do not edit!
FP1
FPZ
FP2
F7
F3
FZ
F4
F8
FC5
FC1
FC2
FC6
M1
T7
C3
CZ
C4
T8
M2
CP5
CP1
CP2
CP6
P7
P3
PZ
P4
P8
POZ
O1
OZ
O2
AF7
AF3
AF4
AF8
F5
F1
F2
F6
FC3
FCZ
FC4
C5
C1
C2
C6
CP3
CPZ
CP4
P5
P1
P2
P6
PO5
PO3
PO4
PO6
FT7
FT8
TP7
TP8
PO7
PO8
Labels END_LISTCan this in MATLAB be converted to .fiff?
The EEG Data is given in the formats shown below. We have not been able
to convert the data. But we know that it can be converted to MATLAB through
FieldTrip.Thank you,
IsaiahHello D,
What I am trying to say is that I did the tutorial, and I am now trying to
do it with other data that I have. I have a file containing the location of
the electrodes in a .elc format and I am wondering how to incorporate these
electrodes onto my head model.I'm not familiar with the .elc format. Were you able to convert the
raw EEG file to fiff format? There may be a tool for doing this
automatically, in the file conversion. Can you tell me more about your
data? What system it was generated by? If you converted the raw EEG
data? What tool you used to convert the data?If there isn't a tool you can always manipulate the raw fif file in
MATLAB and add in the necessary fields to your raw file and save it to
a new file (but first let's find out if there is an automated tool).In addition, where can I find the file containing the lead field matrix?
Just the matrix.The lead field matrix is in the -fwd.fif file you created in the
sample tutorial. The MNE matlab toolbox has a function (the manual
chapter describes how to read it and what the different fields are) if
i remember correctly, it is mne_read_forward_solution(<fname>)).HTH,
DIsaiah
Hi Isaiah,
I'm not really sure from your email what you are having difficulty
with. In "The sample data set" chapter
(http://martinos.org/mne/stable/manual/sampledata.html), there is a
description of how to perform these steps in the following
subsections:The forward solution
The inverse operator decomposition
Interactive analysis
If there is a particular part of this you are having trouble with, can
you describe the problem you are having in more detail.HTH,
DHello D,
I went through the tutorial and I am wondering how I can find the lead
field matrix and create source models from my data in MATLAB after having
made the volume conduction models.Isaiah
Hi Isaiah,
It may be helpful to start with the sample data set chapter (and run
through that example). This will take you step by step through the
basic analysis procedure and show you how to perform each of the
checks etc.HTH,
DHello,
I am following the cook book in order to create head models and find the
lead field matrix. I have just finished using mne_prepare_model_bem. How do
I view my results and how do I prepare this output for
mne_do_forward_solution so that I can find the lead field matrix?Isaiah Smith
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Hi Isaiah,
Conceptually what needs to be done is:
1. Take the ELC file and produce a dummy fif measurement file with measurement info block only. This should contain the electrode locations as digitizer data and channel descriptions for the EEG electrodes with names and locations inserted. Some rough coordinate transformation maybe needed to bring the EEG electrode location data to a RAS-oriented coordinate frame.
2. Align the coordinate MRI and EEG coordinate systems using mne_analyze.
3. With help of the dummy measurement file and the coordinate transformation file produced by mne_analyze you can now produce the gain matrix, often called the lead field matrix even though this is technically an inaccurate term.
I do not have time to write for you the Matlab code right now but maybe this message will excite some volunteer to do so.
Best,
Matti
Thank you, Matti, for the response,
Would it be possible for me to create the code?; I exactly sure how to do what you are referring to in step 1, however.
Isaiah Smith
Thanks, D,
I am waiting on their response.
Isaiah
hi,
you can try to understand:
the create_info function at:
https://github.com/mne-tools/mne-python/blob/master/mne/io/meas_info.py#L790
and use the write_info function at:
https://github.com/mne-tools/mne-python/blob/master/mne/io/meas_info.py#L631
to produce a proper measurement info file.
these functions do not exist out of the box in Matlab.
HTH
Alex
Hello, D,
The group got back to me. The machine was the ASA-Lab fMRI-64-Kit.
Isaiah
Sorry,
I am having a hard time understanding these programs. Alternatively, would it be possible for me to use Python to find the gain matrix, and then later convert the gain matrix into the matlab format?
Isaiah
