Archived FMRI pipeline

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About fMRI data and file types

Raw fMRI data is saved in .dcm (dicom) files. Typically these .dcm files correspond to individual slices, and the resulting 3D image (or a time-series of 3D images) is saved in a .nii (nifti) file. Raw dicom files can be transformed into nifti format using SPM (a MATLAB software package implementing Statistical Parametric Mapping for neuroimaging data) or other software such as MRIcro.

Note that, when handling neuroimaging data, you need to take special care that the orientation of the images is correct.

Standard Preprocessing Steps & The Pipeline

In what follows, we describe the broad stages of fMRI preprocessing. Note that the pipeline saves the data after each intermediate step in newly created files with relevant prefixes.

Slice-Timing Correction

This step corrects for the time-delay between the acquisition of different slices.

Rigid body Correction

This step estimates, characterises and broadly corrects for the effect of head-motion. It is also the step at which one can exclude subjects with excessive head-motion (e.g. more than a voxel size).

Registration to Standard Space

Chose source image, template (EPI), method, image size, voxel size (2x2x2). (This is the 'Normalize' option in SPM. )

Regressing out head motion, CSF, white matter & physiological signals

(In SPM, this is done under '1st level analysis' -> 'Data and design' -> 'Multiple regression'.)

Wavelet Decomposition

A very basic tutorial on wavelets can be found here: [[1]]

For details on the wavelet toolbox in MATLAB, read: [[2]]

The Question of Smoothing

Required before VBM. Important for finding activations regions. Not used when parcellating (for network analysis).

DVARS and the Motion Problem

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