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
- 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:
- Do the six columns represent translationX, translationY,
translationZ and rotationX, rotationY, rotationZ?
- 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
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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
- 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 > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
freesurfer@nmr.mgh.harvard.edu
-
Douglas Greve -
Joseph Dien