Education, tips and tricks to help you conduct better fMRI experiments.
Sure, you can try to fix it during data processing, but you're usually better off fixing the acquisition!

Friday, November 12, 2010

Towards an optimal protocol for resting state fMRI – part II

A couple of weeks ago I used the results in a paper by van Dijk et al. to provide guidance towards a possible optimal/general protocol for resting state fMRI using EPI. That review concluded with the following rough criteria: whole brain coverage, spatial resolution around 3 mm and temporal resolution in the 2-3 seconds range. The largest of the open questions pertained to the interplay between these three specifications, in particular the ability to obtain whole brain (cortex and cerebellum) coverage in the time available, whilst minimizing (we hope) the dropout and distortion that are ever-present features of EPI.

Experimental details:

In what must be considered a disposable experiment on a single subject (medical types might call this a case study), I acquired test data sets with the following parameters:

Siemens 3 T Trio/TIM running VB15, 12-channel HEAD MATRIX coil, ep2d_bold pulse sequence, TR=2500 ms, TE=25 ms, slice thickness=3 mm, gap=0.3 mm, 43 interleaved slices, matrix=64x64, FOV=224x224 mm (except for one test with 192x192 mm), bandwidth=2056 Hz/pixel, echo spacing=0.55 ms, number of volumes=144, fatsat=ON, MoCo=ON, no spatial filters. (See note 1.)