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Not included in the above discussion are specialized fMRI Paradigm Design Tools. These programs help the investigator plan the timing of events and data acquisition needed for the fMRI experiment. They then send appropriate signals to various audiovisual equipment and the MRI scanner to trigger the presentation of stimuli and recording of subject responses.
Basic paradigm design tools are provided by all major MR vendors as part of their standard integrated fMRI packages. Additionally, several of the third party fMRI analysis packages described above also contain design modules. Below is a list of several commonly used toolkits whose primary function is fMRI design:
E-Prime® is a commercial suite of applications from Psychology Software Tools, Inc. of Pittsburgh, PA. The software is widely used for non-MRI psychology and neurophysiology experiments, but also has extensions to allow its use for fMRI. A broad range of routine paradigms can be created a drag-and-drop graphical user interface, but more sophisticated experiments require using their proprietary scripting language (which fortunately, is nearly identical to Visual Basic for Applications). Further information is available at this link.
nordicAktiva is commercially available clinical stimulus and workflow software solution from the Norwegian-based company NordicNeuroLab. They offer not only design software but a complete package of visual, auditory, and response hardware for fMRI experiments. We have historically used this system for clinical eloquent cortex mapping studies. Writing complex new paradigms, however, is moderately difficult as it requires direct editing of the XML code. Further information is available at this link.
Presentation from Neurobehavioral Systems, Inc. of California, is perhaps the easiest to use stimulus delivery and experiment control program for neuroscience with a customizable graphical user interface. It is capable of simultaneously and independently presenting a wide range of stimuli, including images, 2D and 3D graphics, audio, and video. The main limitation is that the program works only under Windows. Further information is available at this link.
The above software is all commercially based, with individual user licenses ranging from several hundred to several thousand dollars. A few free, open-source solutions are available, including PsychoPy from the University of Nottingham (Website) and Psychtoolbox (Website). PsychoPy is written in Python while Psychtoolbox runs on Matlab or Octave.
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List of functional connectivity software. Wikipedia, the free encyclopedia. (Contains a fairly complete list of software for connectivity analysis useful for resting-state fMRI applications)
List of neuroimaging software. Wikipedia, the free encyclopedia. (Contains a fairly complete list of software for fMRI analysis, as well as others tangentially related to fMRI, such as EEG and DTI)
NITRC Resource Repository (NITRC-R). This is a major on-line collaboration environment for neuroinformatics tools and software, including not only fMRI, but PET/SPECT/CT/EEG/MEG/Optical imaging, computational neuroscience, and genomics.
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The FIL Methods Group. SPM12 Manual. Wellcome Trust Center for Neuroimaging, London, 2014.
How is fMRI data processed and analyzed?