[Mne_analysis] Viewing Head Models

Fri Aug 15 18:13:16 EDT 2014

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
On Aug 13, 2014, at 10:01 AM, Matti Hamalainen <msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>> wrote:

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

On Aug 12, 2014, at 6:44 PM, Isaiah C. Smith <Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:

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.
<Screen Shot 2014-08-12 at 2.39.34 PM.png>
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.
<Screen Shot 2014-08-12 at 2.48.55 PM.png>

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.
<Screen Shot 2014-08-12 at 3.21.11 PM.png>

Thank you,
Isaiah

On Aug 12, 2014, at 2:03 PM, dgw <dgwakeman at gmail.com<mailto:dgwakeman at gmail.com>> wrote:

On Tue, Aug 12, 2014 at 4:33 PM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:
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

Isaiah
On Aug 12, 2014, at 5:32 AM, dgw <dgwakeman at gmail.com<mailto:dgwakeman at gmail.com>> wrote:

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

On Mon, Aug 11, 2014 at 11:22 PM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:
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
On Aug 11, 2014, at 6:17 AM, dgw <dgwakeman at gmail.com<mailto:dgwakeman at gmail.com>> wrote:

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

On Fri, Aug 8, 2014 at 6:07 PM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu<mailto:Isaiah.C.Smith.17 at dartmouth.edu>> wrote:
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

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the
e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in
error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu<mailto:msh at nmr.mgh.harvard.edu>
mhamalainen at partners.org<mailto:mhamalainen at partners.org>

_______________________________________________
Mne_analysis mailing list
Mne_analysis at nmr.mgh.harvard.edu<mailto:Mne_analysis at nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140815/eb0a2bf4/attachment.html 