See HBM2009 poster and ArtRepairOverview.pdf for examples of output.
See FMRIPercentSignalChange.pdf for a short tutorial on calculating percent signal change.
See ArtRepairInstructions.html for instructions on running the software.
See MotionandDespike.pdf for motion adjustment and despike.
See FMRIGroupCheck and FMRIGroupOutlier for group quality check programs.
The ArtRepair Toolbox is written by Paul K Mazaika (Center for Interdisciplinary Brain Science Research at Stanford). It originated from the art_detect utility by Paul Mazaika, Susan Whitfield-Gabrieli, and Jeffrey C. Cooper in the Gabrieli Cognitive NeuroSciences Lab at Stanford. Please send any bug reports or comments to mazaika@stanford.edu.
This software is a package of tools to correct motion and artifacts in fMRI data from high motion subjects. Visual review tools are included to quality check for artifacts in the data, and unusual values in single subject estimates. Tools are provided to select subjects that are not confounded by task-correlated motion in order to produce accurate group results. CHANGES in v4 from v3: NEW MOTION ADJUSTMENT program, an alternative to motion regressors. NEW DESPIKE and FILTER program, for voxel-wise robust filtering of noisy data. NEW RMSimage program, summarizes the fluctuations in a time series of images.
These programs assume MATLAB and SPM are installed on your computer. The ArtRepair programs read and write using SPM functions, hence AnalyzeFormat images for SPM2, and NifTi for SPM5 and SPM8. DEVELOPED FOR SPM5: The code was well-tested in SPM5, and is back-compatible with SPM2. Most functions will work for SPM8, but it is not thoroughly tested in that environment. NOT COMPATIBILE with 4D NIFTI files. (Sorry!)
Software Compatibility: We have used the programs in Matlab Versions 6.5 through 7.7, with SPM2 and SPM5, on Linux and Windows XP. It's fairly vanilla Matlab code, but it has not been tested on many different platforms.
BETA-SOFTWARE: This software is made available to promote better understanding and quality review of fMRI data. This software is supplied as is. No formal quality assurance checks were made on the software, and no formal support or maintenance is provided or implied.
SITE SPECIFIC ALGORITHMS: The art_movie visualization program works on most data, however, the automatic detection and repair functions were tuned for use with data from the GE spiral scan used at Lucas Center of Stanford University. You may need to customize internal parameters for a specific site.
Insert the ArtRepair folder into the SPM5, SPM8 or SPM2 toolbox.
Start the ArtRepair program from the toolbox window in SPM,
or from the command line to bring up the GUI for Matlab 7 and later:
>> ArtRepair
or from the command line to bring up the GUI for Matlab 6.5 in the SPM Interactive window:
>> spm_ArtRepairInter
The main programs in ArtRepair can also be started from the command line. Type >>help [command] for more information.
| Command | Nickname | Function |
|---|---|---|
| >> art_movie | "View all data with movie" button | Visualize every voxel of every scan in the data |
| >> art_rms | Finds RMS flucutation on every voxel, and writes an RMSimage of result | |
| >> art_plottimeseries | Plots the timeseries on a voxel. | |
| >> art_slice | "Bad slices: detect and repair" | Repairs bad slices- use before preprocessing |
| >> art_motionregress | Corrects for interpolation errors caused by large motion | |
| >> art_global | "Bad volumes: detect and repair" | Repairs outlier volumes- use just before estimation |
| >> art_despike | Despikes and/or high pass filters an image time series. | |
| >> art_redo | "Apply deweights to existing design" | Reanalyze an existing SPM result with repaired data |
| >> art_percentscale | "Scaling to percent signal change" | Finds scale factors to interpret con image as percent signal change |
| >> art_summary | "Summarize subject contrasts" | Displays the distribution of estimates over the head |
| >> art_groupsummary | "Summarize group contrast" | Displays the distribution of estimates over the head for a group result |
| >> art_groupcheck | "View all data in group SPM.mat" | Displays all subject estimates and ResMS on one voxel
Displays all subject contrast estimates as a movie Runs the art_groupoutlier program for all subjects in the group |
| >> art_groupoutlier | "Find outlier subjects" | Compares contrast estimates of subjects, suggests good subgroups for group analysis. |