Motion correction parameter definitions

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Paul Wright

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Mar 3, 2021, 6:56:34 AM3/3/21
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Hi
I am using the motion parameters estimated by ExploreDTI and would like to know exactly what the numbers represent. I am interested in translation and rotation, but it would be good to know all four in case others need it.

1) What are the axes and directions?
I think:
x: posterior to anterior / roll
y: right to left / pitch
z: inferior to superior / yaw
I am not sure what direction the rotations are in, e.g. does positive y mean pitch back or forward?

2) What are the units?
Is translation in voxels or mm?
Is rotation in degrees or radians?

Many thanks
Paul

Jill Miller

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Mar 3, 2021, 12:06:19 PM3/3/21
to ExploreDTI
Following. Also, would you mind sharing how you got these parameters? 
Thanks!
Jill VM 

Paul Wright

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Mar 4, 2021, 5:16:14 AM3/4/21
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@Jill short answer: load the .mat file and look in the DM_info field.

Here's a script I wrote to get the translation and rotation (can easily add the other two, which I think are squeeze and shear). You can batch it with a wrapper script.

function mpout = E_DTI_MP(filename)
% Save motion parameters from a corrected ExploreDTI data set
% FORMAT: mpout = E_DTI_MDC_graph(filename)
% INPUT:
%   filename    -   ExploreDTI file with motion corrected
% OUTPUT:
%   mpout       -   Movement parameters, images in rows, translation and 
%                   rotation in columns (xt, yt, zt, xr, yr, zr)

if ~exist(filename,'file')
    error('File not found: %s\n\n',filename)
end

fprintf('Loading %s ...', filename)
try
    input = load(filename,'DM_info');
catch
    error('\nCannot find motion correction information. Are you sure this file has been corrected?\n\n')
end
if ~isfield(input,'DM_info')
    error('\nCannot find motion correction information. Are you sure this file has been corrected?\n\n')
end
fprintf('\n')

nimg = length(input.DM_info);
mp = nan(4,3,nimg);
fprintf('Reading data 000 / %03d',nimg)
for img = 1:nimg
    fprintf('\b\b\b\b\b\b\b\b\b%03d / %03d',img,nimg)
    mp(:,:,img) = input.DM_info{img}{1};
end %img
fprintf('\nDone\n\n')

rot = squeeze(mp(1,:,:))';
trans = squeeze(mp(2,:,:))';
mpout = [trans,rot];



Jill Miller

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Mar 5, 2021, 10:52:34 AM3/5/21
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Thanks Paul! I don't know the answer to your other questions, but, I'm happy to know where to find the motion parameters using ExploreDTI now. 

samane pirmoradian

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Apr 14, 2022, 2:06:49 AMApr 14
to ExploreDTI
hi
I want use harvard atlas in explore dti .i dont find this atlas.
please help me.

samane pirmoradian

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Apr 14, 2022, 2:30:30 AMApr 14
to ExploreDTI
hi
I want use harvard atlas in explore dti .i dont find this atlas.
please help me.

On Friday, March 5, 2021 at 7:22:34 PM UTC+3:30 Jill Miller wrote:
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