Can TORTOISE report head motion index?

Submitted by exp.2086 on Thu, 01/02/2020 - 20:54

Can TORTOISE report head motion index? Like max head motion, reported in some papers of DWI data.

Submitted by nayaka on Tue, 01/07/2020 - 10:41



Yes. TORTOISE does output a file that contains information about head motion i.e in the _proc_transformations.txt file. The description of this file and its contents are as follows:

_proc_transformation file: contains information about the transformations for the eddy distortion correction and the motion correction.

1st set of three columns represents the rigid portion of the transformation (in millimeters)
Column #1 > x (for axial data = RL)
Column #2 > y (for axial data = AP)
Column #3 > z (for axial data = IS)

2nd set of three columns represents the rotational (Euler angles) component of the transformation (in radians)
Column #4 > θx
Column #5 > θy
Column #6 > θz



And overall rotation R= Rx Ry Rz

3rd set of three columns represents the weights of the linear affine component of the transformation (shears) (unitless)
Example: if no eddy correction is applied, and you have a horizontal phase encode direction, these values would be x=1, y,z=0
Column #7 > x
Column #8 > y
Column #9 > z

4th set of three columns represents the non-linear component of the transformation (1/millimeters)
Column #10 > xy
Column #11 > xz
Column #12 > yz

The final 2 columns represent the quadratic terms of the eddy distortion correction (1/millimeters)
Column #13 > x2 - y2
Column #14 > 2z2 - x2 - y2

For details on the eddy distortion correction applied, please see; G.K. Rohde, A.S. Barnet, P.J. Basser, S. Marenco, C. Pierpaoli, Comprehensive approach for motion and distortion correction in diffusion weighted MRI. Magnetic Resonance in Medicine, vol. 51, pp. 103-114, 2004.


The rigid transformation of template to structural is in the file: _template_to_str_trans.hd5


All of the above files (_proc_transformations.txt and _template_to_str_trans.hd5) are saved inside the _proc folder and can be accessed during (depending on processing step) and after DIFFPREP has completed.


In addition, all of the above information is graphically represented and stored as a .png inside the QC folder, with a file name ending in '_motion.jpg'. The QC folder will only be generated if you have AFNI installed on your system. An example of the graph can be found in section 8.5 of the following page:



Hope this helps,