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Merged
tiborauer merged 12 commits into from
Jan 5, 2024
Merged

DOT additions #392

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d1b1f33
modifying to handle dot data in addition to epi'
Nov 3, 2023
48f5d28
add outlier filtering
Nov 3, 2023
bbbc369
new lightweight QA plots of functional data w/ outlier flagging
Nov 3, 2023
52bf876
tie stream rename to input instead of output
Nov 7, 2023
84a561c
tweak the output delete warning to include a bit more information
Nov 7, 2023
6316828
use aas_getsettings and aas_getstreams
Nov 13, 2023
0a0fc8a
remove unnecessary isrenameable tags
Nov 13, 2023
a5baa45
apply heuristics to outstream names
Nov 13, 2023
b0d0df2
cosmetic cleanup
Nov 13, 2023
64772c0
fix residual desc
Jan 4, 2024
e246ba8
minor improvements
Jan 4, 2024
97ef5d0
add GVTD outlier thresholding
Jan 4, 2024
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cosmetic cleanup
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Peelle Lab
Peelle Lab committed Nov 13, 2023
commit b0d0df28ffb408347cb7eb0a75414ded866a71fd
13 changes: 2 additions & 11 deletions aa_modules/aamod_dot_fromnifti.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,13 +6,7 @@
<!-- this module generates an dot stream from a nifti file -->
<!-- it reuses aamod_epifromnifti.m rather than writing a dedicated -->
<!-- aamod_dot_fromnifti.m which would largely be identical code -->

<!-- the difference is we create "dot" and "functional_header" outstreams -->
<!-- (rather than "epi" and "epi_dicom_header"); we are gradually modifying -->
<!-- modules that hardcode epi and epi_dicom_header to use renameable streams -->
<!-- (and perhaps adding an aamod_*_dot aliased header) if that functionality -->
<!-- is useful outside of epi processing (ex: aamod_firstlevel_model) -->


<qsub>
<timeBase>0.2</timeBase>
<memoryBase>0.2</memoryBase>
Expand All @@ -24,10 +18,7 @@

<inputstreams>
</inputstreams>

<!-- do not change the order of these streams -->
<!-- (required for renameability) -->


<outputstreams>
<stream>dot</stream>
<stream>dummyscans</stream>
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6 changes: 3 additions & 3 deletions aa_modules/aamod_firstlevel_model_dot.xml
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Expand Up @@ -97,12 +97,12 @@

<inputstreams>
<stream >dot</stream>
<stream isessential='0'>ppi</stream>
<stream isessential='0'>ppi</stream>
<stream isessential='0'>listspikes</stream>
<stream isessential='0'>dot_header</stream>
<stream isessential='0'>realignment_parameter</stream>
<stream isessential='0'>compSignal</stream>
<stream isessential='0'>gd_results</stream>
<stream isessential='0'>compSignal</stream>
<stream isessential='0'>gd_results</stream>
</inputstreams>

<!-- dot outstream used for residuals and will be removed -->
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