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tharpm95 edited this page Apr 5, 2022
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Welcome to the IUSM-ConnPipe wiki! Here you will find links to pages describing the various features of the IU School of Medicine Connectivity Pipeline.
Process T1 Data
- Denoise T1 data
- Perform brain extraction
- Transform into the MNI space
- Perform tissue-type segmentation
- Generate tissue-type masks
- Generate subcortical masks
- Intersect parcellations with tissue data
Process fMRI Data
- Perform spin echo unwarping
- Perform slice timing correction
- Perform motion correction
- Perform registration
- Apply transformations to tissue and parcellation images
- Denoise with ICA-AROMA or HMP regression
- Demean and detrend data
- Identify regions of interest
Process DWI Data
- Perform top-up field estimation
- Perform eddy current correction
- Perform diffusion tensor fitting
- Perform registration
- Generate tissue masks
- Perform Camino tensor modeling and tractography
- Perform deterministic multi-tensor tractography
- Create TrackVis streamline files
- Generate tract-based metric matrices