fmcpr.mcdat are the motion estimates (mm and degrees). mcprextreg is the
motion correction parameters after analysis using a PCA, which is why
there is such a huge difference. By default we use the top 4 components.
doug
On 5/28/13 8:28 PM, Joseph Dien wrote:
I have a follow-up question for this thread. I'm currently assessing whether
to switch from SPM8 to FSFAST. As part of this process, I did a comparison
between the SPM8 and the preproc-sess motion correction outputs but found they
were quite different for the example data I looked at. Furthermore, I found
that the fmcpr.mcdat output and the mcprextreg output are quite different even
though they are both generated by fsfast. The following three charts are for
mcprextreg, fmcpr.mcdat, and SPM8 respectively. Finally, I'm including a
correlation matrix (I don't see any correspondences).
The data are actually two separate sessions with a rest break, resulting in a
discontinuity at the midpoint. The SPM realignment was run separately on each
and as usual the first volume was the reference volume while FSFAST was run on
both sessions as a merged set and I think used the middle volume as its
reference volume. This shouldn't have resulted in such a large difference
between SPM8 and FSFAST though (Ardekani et al 2001 reported they didn't differ
that much in accuracy for SPM99 and AFNI98 versions and my understanding is
that FSFAST uses AFNI's routine) and certainly not between the two FSFAST
outputs.
On the other hand, the magnitude of movement in this example is small so I
guess my main concern is the discrepancy between mcprextreg and fmcpr.mcdat. I
want to make sure I know what I'm looking at and therefore how to use it
properly. I looked up the documentation on AFNI's 3dvolreg
(http://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html). Would I be
correct in thinking that mcprextreg results from the -1Dfile option and
fmcpr.mcdat results from the -dfile option? I can take this to the AFNI
message board once I'm sure where these files came from.
Respectfully,
Joe
Either fmcpr.mcdat or fmc.mcdat
On 09/13/2012 02:07 PM, New Fei Ho wrote:
Hi Doug,
Can you point out the name of file that I should be looking at?
I assumed they were either the mcextreg and mcprextreg output files, but
these only have 6 columns.
Thanks,
New Fei
Hi New Fei, I did some digging and found the docs for the output (pasted
below). Translations (displacement) are in mm, rotations are in degrees
doug
1. n : time point
2. roll : rotation about the I-S axis (degrees CCW)
3. pitch : rotation about the R-L axis (degrees CCW)
4. yaw : rotation about the A-P axis (degrees CCW)
5. dS : displacement in the Superior direction (mm)
6. dL : displacement in the Left direction (mm)
7. dP : displacement in the Posterior direction (mm)
8. rmsold : RMS difference between input frame and reference frame
9. rmsnew : RMS difference between output frame and reference frame
10. trans : translation (mm) = sqrt(dS^2 + dL^2 + dP^2)
On 09/13/2012 11:21 AM, New Fei Ho wrote:
Hi Doug,
To explicitly clarify, does this mean
X: L-R
Y: Anterior-Posterior
Z: Inferior-Superior
And are the values of translation/rotation in millimetres?
Thanks,
New Fei
If by XYZ you mean column, row, slice, then yes. The values are with
respect to the middle time point (or whatever you used as the
template),
it is not the relative difference.
doug
On 09/12/2012 05:37 PM, New Fei Ho wrote:
Hi,
I would like to compare the mean head motion between two groups.
Just to clarify the values found in the mcprextreg file:
1. Do the six columns represent translationX, translationY,
translationZ
and rotationX, rotationY, rotationZ?
2. Are the values found in each time-point (i) absolute, i.e. the
absolute
difference in displacement between this time-point and the middle
time-point, or (ii) relative i.e. difference between consecutive
time-points?
Thanks,
Newfei
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