[Mne_analysis] Viewing Head Models

Sat Aug 16 08:54:21 EDT 2014

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

On Sat, Aug 16, 2014 at 12:13 AM, Isaiah C. Smith
<Isaiah.C.Smith.17 at dartmouth.edu> wrote:
> 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>
> 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> 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
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> 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> wrote:
>
> On Tue, Aug 12, 2014 at 4:33 PM, Isaiah C. Smith
> <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> 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> 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> 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> 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
>
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> ---------
>
> Matti Hamalainen, Ph.D.
> Athinoula A. Martinos Center for Biomedical Imaging
> Massachusetts General Hospital
>
> msh at nmr.mgh.harvard.edu
> mhamalainen at partners.org
>
>
>
>
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> 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
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> but does not contain patient information, please contact the sender and
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> dispose of the e-mail.
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> contains patient information, please contact the Partners Compliance
> HelpLine at
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