Automated linear models for functional neuroimaging data
Project description
GLM-Express
This is a package for modeling functional neuroimaging tasks. As the name implies, it's optimized to be simple and straightforward! The task_information.json
file stores all of the regressors and modeling specifications for each task; modifying this file allows you to test a range of analytical outcomes.
Included
This package comes equipped with the following modeling objects:
Subject
is a first-level modeler for subject-specific functional neuroimaging dataGroupLevel
is a second-level modeler that is optimized to aggregate contrast maps derived by theSubject
objectAggregator
applies first-level models to all subjects in your BIDS project (not efficient for larger datasets)
In Development
RestingState
object is currently in development, for analyses of subject-level resting state functional connectivity
Assumptions
We assume the following about your data:
- Your data is in valid
BIDS
format - Your data has been preprocessed via
fmriprep
- Your preprocessed data are stored in a
derivatives
folder nested in yourBIDS
project - You have adequate events TSV files for all of your functional tasks
- Any parametric modulators are stored within each event file
- Otherwise, you can build custom design matrices and feed them into the modeling function
About task_information.json
Glossary of keys in the task_information
file; manipulating these allow you to quickly and effectively customize your modeling parameters without editing any source code
tr
: Repetition time (defined here, but can be overriden for any one subject)excludes
: Subjects in your project you need to exclude for a given taskcondition_identifier
: Column in your events file that denotes trial type; NOTE this will be changed totrial_type
in the scriptconfound_regressors
: Regressors to include fromfmriprep
outputmodulators
: Parametric modulators to weight trial type (these should be in your events file)block_identifier
: Column in your events file that denotes block type; defaults tonull
design_contrasts
: Your defined contrasts! Include as few or as many as you see fit
Project details
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