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⇤ ← Revision 1 as of 2015-05-08 12:12:16
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| The process will identify when a subject has moved during a recording. This runs only on continuous, raw recordings for CTF MEG where continuous head localization is recorded (and the HLC channels are collected.) This process is currently being tested. If you find a bug or have other comments related to its performance, please provide comments here or on the Forum. | The process will identify when a subject has moved during a recording. This runs only on continuous, raw recordings for CTF MEG where continuous head localization is recorded (and the HLC channels are collected.) This process is currently being tested. If you find a bug or have other comments related to its performance, please provide comments here or on the Forum. |
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| 1. Detect the movement. This will go through the recording and mark short transient movements (<5 seconds) as 'BAD' and mark the beginning of longer movements where the file can be cut. It generates a file called headpostions.txt which contains the recommended locations where the file should be cut and the new head position that should be written to the new file. 1. Cut the recording into shorter recordings using the CTF software. Use the headpositions.txt file to know where to make the new .ds files and what the new head position should be. This is done outside the Brainstorm software, using the CTF commandline program newDs. You can see an example here |
1. Detect the movement. This will go through the recording and mark short transient movements (<5 seconds) as 'BAD' and mark the beginning of longer movements where the file can be cut. It generates a file called headpostions.txt which contains the recommended locations where the file should be cut and the new head position that should be written to the new file. 1. Cut the recording into shorter recordings using the CTF software. Use the headpositions.txt file to know where to make the new .ds files and what the new head position should be. This is done outside the Brainstorm software, using the CTF commandline program newDs. You can see an example here: {{attachment:split_ctf_recording.m}} To run the movement detection, put the raw link in the Process1 box -> Run -> Events -> Detect movement [Experimental] |
Detect Movement
The process will identify when a subject has moved during a recording. This runs only on continuous, raw recordings for CTF MEG where continuous head localization is recorded (and the HLC channels are collected.) This process is currently being tested. If you find a bug or have other comments related to its performance, please provide comments here or on the Forum.
The end goal if this detection is to find when the subject has moved beyond an acceptable limit and cut the longer recordings in to shorter recording and assign a new head position to each. There are two steps:
1. Detect the movement. This will go through the recording and mark short transient movements (<5 seconds) as 'BAD' and mark the beginning of longer movements where the file can be cut. It generates a file called headpostions.txt which contains the recommended locations where the file should be cut and the new head position that should be written to the new file.
1 function split_ctf_recording(origDS, newDSpath, sampRate, totalTrials)
2 % splits CTF .ds recordings into chunks according to the head
3 % movement. Run the Brainstorm process 'process_detect_movement.m' first to get the
4 % headpositions.txt file
5 %
6 % Inputs: origDS - file to split
7 % newDSpath - directory where the new file will be written
8 % sampRate - sampling rate of the data set
9 % totalTrial - total trials in the file
10 %
11 % Elizabeth Bock 2013-2015
12
13 %% Info
14 info = load(fullfile(origDS, 'headpositions.txt'));
15 [p,n] = fileparts(origDS);
16
17 posFile = dir([origDS '/*.pos']);
18 posFile = fullfile(origDS, posFile.name);
19
20 % find files that are > 5 secs
21 len = diff(info(:,1));
22 ind = find(len > sampRate*5);
23 disp(['Files ' num2str(ind') ' are greater than 5 seconds']);
24
25 %% split first chunk
26 if info(1,1) == 1
27 disp('first chunk has a new head position also')
28 % go directly to the 'N-1 chunks' to get the new head position
29 else
30 st = 1;
31 en = round(info(1,1)/sampRate) - 1;
32 newDS = [newDSpath '/' n '_s1.ds'];
33 command = ['ctf newDs -includeTrialRange ' num2str(st) ' ' num2str(en) ' ' origDS ' ' newDS];
34 system(command)
35 try
36 copyfile(posFile,newDS)
37 catch
38 disp (['cannot copy pos file to ' newDS])
39 end
40 end
41
42
43 %% next N-1 chunks
44 for ii = 1:size(info,1) - 1
45 % split next chunk
46 st = max(1,round(info(ii,1)/sampRate));
47 en = round(info(ii+1,1)/sampRate) - 1;
48 newDS = [newDSpath '/' n '_s' num2str(ii+1) '.ds'];
49 command = ['ctf newDs -includeTrialRange ' num2str(st) ' ' num2str(en) ' ' origDS ' ' newDS];
50 system(command)
51
52 % update head position (need mm for input to this function)
53 na = info(ii,3:5).*1000;
54 le = info(ii,6:8).*1000;
55 re = info(ii,9:11).*1000;
56 command = ['ctf changeHeadPos -na ' num2str(na) ' -le ' num2str(le) ' -re ' num2str(re) ' ' newDS];
57 system(command)
58
59 try
60 copyfile(posFile,newDS)
61 catch
62 disp (['cannot copy pos file to ' newDS])
63 end
64 end
65
66 %% last chunk
67 ind = size(info,1);
68 st = round(info(ind,1)/sampRate);
69 en = totalTrials;
70 newDS = [newDSpath '/' n '_s' num2str(ind+1) '.ds'];
71 command = ['ctf newDs -includeTrialRange ' num2str(st) ' ' num2str(en) ' ' origDS ' ' newDS];
72 system(command)
73
74 % update head position
75 na = info(ind,3:5).*1000;
76 le = info(ind,6:8).*1000;
77 re = info(ind,9:11).*1000;
78 command = ['ctf changeHeadPos -na ' num2str(na) ' -le ' num2str(le) ' -re ' num2str(re) ' ' newDS];
79 system(command)
80
81 try
82 copyfile(posFile,newDS)
83 catch
84 disp (['cannot copy pos file to ' newDS])
85 end
To run the movement detection, put the raw link in the Process1 box -> Run -> Events -> Detect movement [Experimental]