Dear Dr. Smith and Dr. Behrens:
First, thank you for developing the FDT Diffusion Toolbox -- it's a great software.
I would appreciate your help / advice with respect to the tutorial data that came with FSL,
specifically the FDT tutorial data (located in the folders 'fdt/subj1' and 'fdt/sub1.bedpost')
I have followed the FDT practical using the tutorial data provided on the website, and would like to
get more information about how the provided diffusion-weighted data was collected and pre-
processed before being distributed. I would like to get this information to understand how our
research team can get our own data to a similar level / quality as the tutorial data in order to
maximize subsequent DTI analysis and fiber tracking results in FDT. I am very grateful for your
help in advance.
Specifically:
1) Which scanner was the diffusion data collected on? Was it a GE scanner?
2) What scanner parameters were used to collect the diffusion data?
a. It looks like 65 volumes comprise the DTI data; does this mean that that data contains 64
diffusion-weighted volumes (representing 64 gradient directions) and 1 non-weighted volume?
b. Was the tutorial data constructed from a single DTI scan or were multiple scans averaged to
remove noise? If so, how many scans were averaged?
c. The diffusion data has a voxel size of 2 x 2 x 2 mm; is this the voxel size of original / raw data
as it came out of the scanner ? if not, what was the original voxel size and how (using what
program and resampling method) was the data re-sampled / interpolated?
d. What inter-slice spacing was used for the DTI dataset?
e. What was the magnetic field strength of scanner used?
f. What DTI sequence was used to collect data? (standard echo-planar imaging, line-scan diffusion
imaging, FLAIR-DTI, etc.)
3) How was the raw / original DTI data prepared / pre-processed to obtain the supplied tutorial
data?
a. Was the raw data resampled / re-sliced ? If so, how?
b. Was the raw data averaged across multiple scans to remove noise?
c. Were any specific steps taken (in addition to the Eddy Current Correction in FDT) to remove /
correct for (1) motion artifacts and (2) image distortion artifacts in the raw DTI data? If so, what
software was used to do this?
d. Were any other steps / parameters implemented to remove noise / artifacts in the raw DTI data,
either during scanning or during pre-processing of the data?
Thank you very much for your time and help. I look forward to hearing from you soon.
Sincerely,
Igor Korolev
PhD student
Neuroscience Program
Michigan State University.
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