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megq edited this page Jun 8, 2017 · 22 revisions

Welcome to the CONTE wiki!

If you're interested in learning all about CONTE fMRI I would read the wikis in the following order:

  1. Fear Conditioning Paradigm to learn about the task

  2. Model Overview to learn an overview of what analysis models were run on CONTE and what they mean

  3. FSL Analysis Pipeline to then learn how to run those models described in wiki #2 in FSL Feat

  4. XCP Pipeline to alternatively learn how to run those models described in wiki #2 using the XCP Engine

The FreeSurfer wikis detail you guessed it, FreeSurfer structural processing. The XCP Engine also details structural processing but for ANTS, gmd and jlf volume.

The ratings wiki will give you more information on the design and processing of the Behavioral task Ratings.

These wikis were written by MQ (and EEG by PR) in 2017 to record information about CONTE before leaving the BBL. This is why the wikis only really focus on run1 fear conditioning, freesurfer, EEG, and behavioral ratings design, processing, and analysis. CONTE also has a reversal fear conditioning paradigm, resting BOLD imaging, and pupilometry as well as clinical and CNB data. However, that information is not detailed in these wikis as MQ did not process or analyze that data.

All CONTE aggregated data is stored in the CONTE2 project on RedCap. The raw data files, processed data, and scripts are on both monstrum (/import/monstrum/conte_815814) and on CFN (/data/joy/BBL/studies/conte and /data/joy/BBL/projects/conteReproc2017). If you are new to CONTE and looking for more organized and finalized scripts and data you should work off of CFN rather than monstrum. This is why these wikis, although they mention some monstrum paths, focus on CFN paths and processing. Monstrum contains all that is on CFN (except for XCP Engine processing) but it is quite messy and also contains a lot of other intermediary analyses, data, and processing that may make sorting through or continuing the project more confusing. However, if you're looking for a script or analysis that used to be run to revive it, it will live on monstrum and not on CFN.

Dan Wolf and Kosha Ruparel would be the best individuals to provide information on fMRI CONTE that is missing and must be known, Karthik also handled the pupilometry analyses and so he would be a useful resource for that. Sean Gallagher and Monica Calkins handle the clinical side, and Bruce Turetsky oversees EEG (since Petra Rupert is also leaving the BBL this June 2017).

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