Despiking

[Alfonso Fajardo]

Hello:

Im using  cpac_v1.0.1a_17 through a singularity container in a cluster grid (non-gui). Unfortunetely most recent version is not running and I still have to figure out why. Anyway, I want to configure my pipeline to run de-spiking instead of scrubbing. Does the version i use allow this option?. How may I set my pipeline_config.yml file in order to do this?

Thankfully,

Alfonso

[Steven Giavasis]

Hi Alfonso,

De-spiking became available in C-PAC version 1.0.2 and later. There is currently a C-PAC v1.1.0 container available- I would recommend using this.

To configure a pipeline config YAML to run de-spiking, enter these keys (and modify the other options as necessary):

# Remove or regress out volumes exhibiting excessive motion.

# Options: ['Off'], ['De-Spiking'] or ['Scrubbing']

runMotionSpike :  ['De-Spiking']

# (Motion Spike De-Noising only) Choose which Framewise Displacement (FD) calculation to apply the threshold to during de-spiking or scrubbing.

# Options: ['Jenkinson'] or ['Power']

fdCalc :  ['Jenkinson']

# (Motion Spike De-Noising only) Specify the maximum acceptable Framewise Displacement (FD) in millimeters.

# Any volume exhibiting FD greater than the value will be regressed out or scrubbed.

spikeThreshold : [0.5]

# (Motion Spike De-Noising only) Number of volumes to de-spike or scrub preceding a volume with excessive FD.

numRemovePrecedingFrames :  1

# (Motion Spike De-Noising only) Number of volumes to de-spike or scrub subsequent to a volume with excessive FD.

numRemoveSubsequentFrames :  2

Hope this helps.

Best,

Steve