Can TORTOISE report head motion index?

Submitted by exp.2086 on

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,