Improvements and tweaks to the preprocessing workflow #32
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absolute deviation). Previously, it used mean and standard deviation.
Importantly, this means that the your intensity threshold should be
adjusted by a scaling factor to provide a similarly stringent threshold.
As a general rule of thumb, 1 SD is about 1.48 MADs.
spike_threshod
in the experiment file. It is also in units of medianabsolute deviation. It is
None
by default, indicating that no volumeswill be excluded for white noise spikes. Additionally, a plot that can be
used to diagnose spikes has been added to the artifact detection report.
intensity based (although the intensity threshold was determined within a
mask output by BET). Now, the Freesurfer segmentation is used to define
an anatomical brain mask, which is then transformed into native run
space. This should avoid losing voxels in magnetic susceptibility areas
like ventral temporal cortex.
interfaces and added some utility functions to make this code simpler.