dowdlelt / meica_tool Goto Github PK

The plots of E2 vs MEDN are a bit tricky, because the MEDN time series will typically be detrended and to some extent highpass filtered due to MEICA. This may or may not bias these figures to make MEDN look even better.

A simple detrending might be a solution.

For later, easy QC:
Add T2star figures
Add vein figures

Uses the motion.1D file to plot motion, and in turn Framewise Displacement. Unfortunately the motion calculation is produced by the 3dvolreg (https://afni.nimh.nih.gov/pub/dist/doc/program_help/3dvolreg.html)
option -dfile which has the following attributes:
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 }

so, have to correct plots, and supply information to bramila_framewise correctly.

While the plots are nice, it would be more useful to know the TSNR in grey matter, separately from white matter and CSF. Need to see if MEICA segments the tissues. If not, could use the SPM segmentation, assuming the delay is acceptable.