BDP: BrainSuite Diffusion Pipeline. Divya Varadarajan
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1 BDP: BrainSuite Diffusion Pipeline Divya Varadarajan
2 BDP Mouse spinal chord axial diffusivity (DTI) MPRAGE Diffusion dataset Joong Hee Kim, MRM 2016 T1/DWI coregistration Distortion correction Diffusion modeling Whole brain tractography Connectivity analysis
3 BrainSuite Diffusion Tools T1/DWI coregistration Distortion correction Diffusion modeling Whole brain tractography Connectivity analysis BrainSuite Diffusion Pipeline Command line tool (bdp.exe / bdp.sh) BrainSuite GUI Allows user interaction Highly flexible
4 BDP command line
5 BrainSuite GUI
6 EPI distortion in diffusion MRI MPRAGE b=0 image Field inhomogeneity Overlay with edges MPRAGE b=0 image MPRAGE b=0 image
7 Distortion correction in BDP 1. Fieldmap based fieldmap correction <fname.nii.gz> 2. Registration based (default) Uses structural image to estimate distortion field Does not require a field inhomogeneity map T1/DWI coregistration Distortion correction Constrained non rigid registration 3. no distortion correction (Only Rigid) / no structural registration Different distortion correction method, eg. IPED. No distortion e.g. ex vivo study Non brain data e.g. heart, thigh etc. No MPRAGE and no fieldmap Bhushan et al., 2012, 2014, 2015
8 Distortion correction in BDP Distorted After correction Color FA overlaid on MPRAGE image after correction
9 Diffusion modeling Diffusion tensor Low resolution sampling High resolution single shell sampling Arbitrary sampling E.g. Multi shell/cartesian GQI ODFs Yeh 2010 FRACT ODFs Haldar & Leahy, 2012, 2013 FRT ODFs Tuch 2004, Descoteaux D SHORE ODFs Ozarslan 2009, Merlet 2013
10 FA image Color FA Low resolution /High resolution single shell data Diffusion parameters FA map MD map Useful for quantitative diffusion studies Bad for Crossing fibers MD Diffusion tensor
11 FA image High resolution single shell data GFA Diffusion parameters GFA map Useful in quantitative diffusion studies Detects Crossing fibers FRT ODF (min max norm.) Tuch 2004, Descoteaux 2007
12 FA image High resolution single shell data Tractography Detects Crossing fibers Better angular resolution than FRT Recommended for Tractography FRACT ODF (min max norm.) Haldar & Leahy, 2012, 2013
13 FA image High resolution data Arbitrary sampling scheme Multi shell sampling Cartesian sampling Custom sampling Detects Crossing fibers 3DSHORE ODF (min max norm.) Ozarslan 2009, Merlet 2013
14 FA image High resolution data Arbitrary sampling scheme Multi shell sampling Cartesian sampling Custom sampling Detects Crossing fibers GQI ODF (min max norm.) Yeh 2010
15 FA image High resolution data Arbitrary sampling scheme Multi shell sampling Cartesian sampling Custom sampling Detects Crossing fibers 3DSHORE ODF
16 FA image High resolution data Arbitrary sampling scheme Multi shell sampling Cartesian sampling Custom sampling Detects Crossing fibers GQI ODF
17 Choosing the Diffusion model Know your data Figure out the relevant diffusion models Example : Multi shell data > DTI, FRT, FRACT be careful! BDP will warn you during sampling modeling mismatch
18 Choosing the Diffusion model Try the relevant models on a subset Look for features that your application needs. Example : Tractography depends on the angular resolution of ODFs HCP Multi shell Dataset Fractional anisotropy FRACT (b=3000 sec/mm^2) Recommendation : Quantitative studies : DTI, Use b=1000 shell For tractography with HCP data use b=3000 shell along with FRACT ODFs. 3DSHORE Varadarajan & Haldar, OHBM 2017 ( Poster 2999) )
19 Running BDP BDP executable location Mac: /Applications/BrainSuite17a/bdp/bdp.sh Windows: C:\Program Files\BrainSuite17a\bdp\bdp.exe Typical syntax bdp.sh <BFC File> [Optional Flags] nii <4D DWI NIfTI> \ bvec <Gradient file> bval <b value file> Example bdp.sh bfc.nii.gz tensor odf \ nii dwi.nii.gz bvec dwi.bvec \ bval dwi.bval (See next section and website for more details)
20 BDP: Flexible flags.t1_coord.d_coord >50 optional flags Supports several types of diffusion data Works without anatomical image
21 Frequently used flags Software support flags --help or h - Prints out description of all BDP flags and BDP version. --check-for-updates - Connects to BrainSuite server to check if a new version of BDP is available Distortion correction flags --dir=<direction> - Define phase encoding direction --fieldmap-correction <fname.nii.gz> - Fieldmap in rad/sec --echo-spacing=<t> - Echo spacing in sec Registration flags --no-structural-registration Run BDP in diffusion space --rigid-reg-measure <measure> Similarity measure for rigid registration Diffusion modeling flags --frt,--fract,--tensors,--3dshore,--gqi - DTI and ODF methods I/O flags --nii Input DWI file --output-subdir Output subdirectory --output diffusion coordinates Outputs in diffusion coordinates Of course online documentation:
22 User friendly interface Summary <fileprefix>.bdpsummary.txt
23 User friendly interface Command line output Always verbose with relevant important information
24 User friendly interface Error! Forums
25 BDP outputs files/
26 Example study Regional Susceptibility to Chronic Anemia in WM Microstructure Using Diffusion Tensor Imaging S Choi, AM Bush, M Borzage, AA Joshi, TD Coates, RM Leahy, JC Wood, 58th American Society of Hematology Annual Meeting and Exposition (ASH), San Diego, 2016, 3640
27 BDP Documentation: Detailed flag description:
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