Hi-

Sure. It would help to probably see your 3dvolreg command, to see the options you are using in detail; I can guess at some.

Firstly, this AFNI Academy playlist on various aspects of alignment might be a useful reference. It includes videos on EPI-EPI alignment (covering a lot of 3dvolreg) and EPI-anatomical alignment (covering more about 3dAllineate).

The `*.aff12.1D`

files store the 12 degrees of freedom (DFs) of a linear affine transform: there are nine numbers of the 3x3 rotation/shear/scale matrix and three numbers of 3x1 translation vector. This style of output (using `1Dmatrix_save ..`

in either 3dAllineate or 3dvolreg) does *not* have the individual rotation/shear/scale/translation parameters. It just has the matrix+vector elements. To store the individual parameters, one would use `-1Dparam_save ..`

in 3dAllineate; in 3dvolreg, one would can just save the rigid body (6 DF) parameters individually, with `-dfile ..`

or `-1Dfile ..`

.

In general, it is not supereasy/straightforward to decompose the 3x3 + 3x1 matrix+vector elements into shear/rotation/etc. parameters. Going from parameters to matrix elements is OK, for what it's worth. There is an option in `cat_matvec`

to get the "rigid equivalent" matrix+vector transformation of the 12 DF affine, using `-P`

:

```
-P = Do a polar decomposition on the 3x3 matrix part
of the mfile. This would result in an orthogonal
matrix (rotation only, no scaling) Q that is closest,
in the Frobenius distance sense, to the input matrix A.
Note: if A = R * S * E, where R, S and E are the Rotation,
Scale, and shEar matrices, respctively, Q does not
necessarily equal R because of interaction; Each of R,
S and E affects most of the columns in matrix A.
```

I'm not sure what a "MD" file is from 3dvolreg?

If you have 6 parameters in a file from 3dvolreg, I'm guessing you sued `-1Dfile ..`

, and the help describes the ordering and what each volume means:

```
...
roll = rotation about the I-S axis }
pitch = rotation about the R-L axis } degrees CCW
yaw = rotation about the A-P axis }
dS = displacement in the Superior direction }
dL = displacement in the Left direction } mm
dP = displacement in the Posterior direction }
...
** roll = shaking head 'no' left-right
** pitch = nodding head 'yes' up-down
** yaw = wobbling head sideways (ear toward shoulder)
...
-1Dfile ename Save the motion parameters ONLY in file 'ename'.
The output is in 6 ASCII formatted columns:
roll pitch yaw dS dL dP
...
```

--pt