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Improvements and tweaks to the preprocessing workflow #32

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merged 15 commits into from
Jun 11, 2014
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@mwaskom mwaskom commented Jun 10, 2014

  • The artifact detection code now uses robust metrics (median and median
    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.
  • Added white noise spike detection. This is controlled through the
    spike_threshod in the experiment file. It is also in units of median
    absolute deviation. It is None by default, indicating that no volumes
    will be excluded for white noise spikes. Additionally, a plot that can be
    used to diagnose spikes has been added to the artifact detection report.
  • Changed the derivation of the brain mask. Previously, this mask was
    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.
  • Otherwise updated the preproc report with better summary figures.
  • Also converted most of the preproc workflow functions to full-fledged
    interfaces and added some utility functions to make this code simpler.

@mwaskom mwaskom changed the title Better preproc Improvements and tweaks to the preprocessing workflow Jun 10, 2014
mwaskom added a commit that referenced this pull request Jun 11, 2014
Improvements and tweaks to the preprocessing workflow
@mwaskom mwaskom merged commit 1db844a into master Jun 11, 2014
@mwaskom mwaskom deleted the better_preproc branch June 11, 2014 19:21
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