Frequently Asked Questions

BrainSuite Diffusion Pipeline

    1. What are the supported (input) file formats?
      • BDP works best with input image volume in NIfTI format. See BDP file-format for more details.
    2. What are system requirements for BDP?
      • See “System Requirements” section in BDP technical details. In addition note that system requirement for running tractography is independent from that of running BDP and can change depending on diffusion model and dataset used.
    3. Where can I download sample datasets?
      • Only diffusion data – click here
      • Diffusion data along with extracted surfaces and SVReg labels – click here
      • Note about the above dataset: All the datasets were produced from the Beijing Enhanced data, Beijing Normal University, State Key Laboratory of Cognitive Neuroscience and Learning Enhanced Sample, which is available under a Creative Commons Attribution – Non-Commercial license (CC-BY). For more details please see: http://fcon_1000.projects.nitrc.org/indi/retro/BeijingEnhanced.html.
    4. What types of diffusion MRI data can be used with BDP? What is the convention of diffusion gradient direction (.bvec file)?
      • See BDP technical details for detailed description of supported diffusion MRI datasets and diffusion gradient directions.
    5. Where are the flag description?
    6. What does “RAS” in file names mean?
      • BDP saves most image volumes in NIfTI-1 format with “RAS” convention i.e. the image data is stored such that the most rapidly increasing voxel index increases along Right side of subject, followed by Anterior side and then by Superior side of the subject. More precisely,  the image is saved in an orientation which is closest to the ‘canonical spaceand the (s-form) rotation matrix in NIfTI header is set as close to identity matrix as possible (ignoring scaling).
    7. What are the unit of reported quantitative diffusion parameters in output images (MD etc.) and statistics files?
      • BDP reports diffusivity (MD, axial, radial, L2 and L3) in a unit which is reciprocal inverse of the units of input b-value specified in .bval file.
    8. What are different types of distortion correction supported by BDP?
      • There are three different modes of distortion correction (1) Registration based distortion correction, (2) Fieldmap based distortion correction, and (3) No distortion correction. See Co-registration page for more detailed description.
    9. Does BDP Co-registration correct the input diffusion data for eddy-current or motion artifacts?
      • As of now, BDP does not attempt to correct the input data for any eddy-current or motion artifact. If your dataset is affected by these artifacts then you may have to first correct your dataset for these artifacts outside BrainSuite. We plan to develop and  include these correction methods in future.
    10. Can I use diffusion MRI data split over multiple runs/acquisitions with BDP?
    11. If you are using NIfTI-1 images as input, you have to first combine images (and corresponding gradient and b-value files) from multiple scans into one single 4D NIfTI-1 file. mergeDWIs from BDP Add-ons can be used for this purpose.