https://github.com/mwaskom/fluid_nipype

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NiPype code for gfluid project

README

Fluid Intelligence Project Analysis Code
========================================

Functional Analysis
-------------------

``fluid_fmri.py`` --
Main interface for functional analysis.
Uses code from workflows and experiment packages.

``fluid_resting.py`` --
Interface for resting state preprocessing and registration.
Uses code from workflows package.

Structural Analysis
-------------------

``fluid_flash.py`` --
Analysis of multispectral FLASH images.

``fluid_tbss.py`` --
Enhanced TBSS (tract-based segmentation statistics) workflow for DTI/R1 analysis

``fluid_morph.py`` --
Freesurfer cortical-reconstruction-based morphometric analysis.

``fluid_vbm.py`` --
Direct Nipype implementation of FSL VBM protocol.

``fluid_dti.py`` --
VBM Analysis of DTI-based images.

Workflows
---------
Package with workflow modules.
Should be entirely independent of anything Gfluid relevant.

``preproc.py`` --
Preprocessing.

``fsl_model.py`` --
First-level FSL modelfitting .

``registration.py`` --
Application of normalization parameters and sampling to surface manifolds.

``fixed_fx.py`` --
Second-level (within-subject) fixed-effect analysis.

``resting_preproc.py`` --
Preprocessing for resting-state scans.
Will be deprecated soon when ``preproc.py`` is made more flexible.

``interfaces.py`` --
A few custom interfaces for scripts that only exist at MIT.

``utility.py`` --
Some utility classes/functions that are useful in workflows.

Experiment
----------
Package with modules containing paradigm information.

``iq.py`` --
fMRI paradigm with fluid reasoning tasks.

``nback.py`` --
Dual (auditory letter-matching/spatial) N-Back task.

``mot_block.py`` --
Blocked multiple object tracking.

``mot_jitter.py`` --
Event-related multiple object tracking.

Misc
----

``unpack_dicoms.py`` --
NiPype script to convert DICOM files to nifti/mgh format and perform
structural preprocessing.

``generate_parfiles.py`` --
Script to read Psychtoolbox experiment files and create FSL parfiles.

``prepapre_fieldmaps.py`` --
Siemems/Fluid specific B0 fieldmap preprocessing.

``fluid_utility.py`` --
Assorted functions used in our Nipype scripts.

Note
----

The code contained in this repository is subject to change at any time.