ENH: Confound model enhancement #1586
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PIN nipype and niworkflows
[MAINT] Repin dependencies
oesteban
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Apr 29, 2019
This PR updates the fMRIPrep report specification to include derivatives generated in the context of nipreps/fmriprep#1586
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oesteban
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May 3, 2019
| @@ -173,7 +173,7 @@ motion-correction parameters estimated by fMRIPrep; | |||
| if present, ``non_steady_state_outlier_XX`` columns indicate non-steady state volumes with a single | |||
| ``1`` value and ``0`` elsewhere (*i.e.*, there is one ``non_steady_state_outlier_XX`` column per | |||
| outlier/volume); | |||
| six noise components are calculated using :abbr:`CompCor (Component Based Noise Correction)`, | |||
| additional noise components are calculated using :abbr:`CompCor (Component Based Noise Correction)`, | |||
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@rciric I feel we will need to expand this and elaborate a bit more about what components were dropped, how they are denoted and why they were dropped. I'd be fine to do that on another PR (with a branch called docs/<whatever> we would be saving a lot of CircleCI cycles).
| signals were expanded with the inclusion of temporal derivatives and | ||
| quadratic terms for each [@confounds_satterthwaite_2013]. | ||
| Frames that exceeded a threshold of {fd} mm FD or {dv} standardised DVARS | ||
| were classified as motion outliers. |
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Suggested change
| were classified as motion outliers. | |
| were annotated as motion outliers. |
maybe better?
| the aforementioned mask and the union of CSF and WM masks calculated | ||
| in T1w space, after their projection to the native space of each | ||
| functional run (using the inverse BOLD-to-T1w transformation). | ||
| functional run (using the inverse BOLD-to-T1w transformation). Components | ||
| are also calculated separately within the WM and CSF masks. |
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As in my previous comment (i.e. to-do in another PR), we should update the boilerplate to mention the component selection strategy. If that is described in Satterthwaite 2013, it'd be pertinent to also add the reference here.
effigies
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May 3, 2019
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Good job @rciric! |
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Replaces #1487 after my mistake forcing a push.