Hi - The fact that the first 2 parameters are all zero (translation and rotation) means that it didn't find the file that it expects to derive those parameters from. Currently, this is the eddy_correct log file that contains the affine registration matrices from each DWI volume to the first volume. This file is called dmri/dwi.ecclog and it is produced by the first of the pre-processing steps of trac-all (the -prep step).
The other 2 motion parameters are "0 1" when there are no slices with excessive signal drop-out found in the DWIs, which is an entirely plausible scenario and hopefully the case for most of your data sets. The motion parameters that trac-all extracts are described here: http://www.sciencedirect.com/science/article/pii/S1053811913011312 Hope this helps, a.y On Wed, 10 Dec 2014, Yuwen Hung wrote: > Hi, > I ran our pipeline script that contains DTI_prep and Tracula, and when I > extracted the individual motion data, they are mostly zeros (see below) > Is this normal? If this is a problem, can anyone please let me know if there > any way to fix this (e.g. re-run the motion script..)? > Your help would be greatly appreciated! > > ps: I just need to examine the motions between 2 groups (below are all data > from the 2 groups). > > AvgTranslation AvgRotation PercentBadSlices AvgDropoutScore > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0.0419463 1.02647 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0.370763 1.23369 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0.414365 1.13071 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > 0 0 0 1 > > Thanks so much for helping! > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
