Auto Analysis Pipeline //
The Mind Research Network has an automated data pipeline that collects, organizes, and processes 3T MR data. If researchers use COINS and follow setup procedures, a level one data analysis can be performed automatically with minimal effort. An analysis has been worked out for fMRI, DTI, VBM, MRS, ASL, and Freesurfer and can be tailored to individual studies. Researchers must upload fMRI behavioral data into COINS along with any important notes or problems about the scan to be archived. Once the scan session data reaches the network archive drive, the data is picked up by automatic scripts at 2am the day following the scan. If requested, the researcher can receive emails about their scan and analysis. One email goes out regarding all scans performed on the scanner for that day. One email will notify researched on completion of the fMRI, VPM, and DTI analysis, and a second email will notify of the completion of a Freesurfer analysis. MRN provides staff to help researchers get approval to scan, use a standard scan protocol, and automate data analysis. You can also request to receive raw data, which can be provided in CD format.
fMRI preprocessing = A standard SPM pipeline is used to preprocess the data. INRIAlign is used to realign the data and SPM is used to slicetime correct, normalize, and smooth the data (10mm). Parameters can be tailored to an individual analysis.
fMRI stats processing = Stimulus timing can be extracted automatically from Presentation, Eprime, or CIRC files and individual stats can be setup to run after each scan if a stats model is worked out prior to the analysis. An SPM stats model can be run on all data after all data sets are collected, but if contrasts are thought through before the scans, corrections can be made to the stimulus presentation if they are caught during test scans at the beginning of the study.
Diffusion Tensor Imaging(DTI) = Use FSL for DTI analysis and FLS tbss to complete fractional anisotropy(FA) maps.
VBM = Averaged MPRAGE SPM analysis provides volume and density results for grey matter and white matter tissues.
FreeSurfer = Anatomical analysis that provides cortical and subcortical results.
Spectroscopy data = Provides SVS and CSI archive along with auto analysis using LC Model and applying in-house developed partial volume correction.