DSI Preprocessing

[Sahil Bajaj]

Hi everyone,

I am very new to DSI studio and actually this is my first time I am handling DSI data. Can someone please guide me from 1st step (preprocessing) to track fibers or if some one has some document stating steps how to use DSI studio. I tried to play with DSI studio and got fibers using following steps but I am not sure if I am on right path:

1). Converted .dcm files to .nii using dcm2nii software and got .bval and .bvec files.

2). Loaded .nii data and .bval. .bvec to DSI studio which gives .src file.

3). Opened .src files during reconstruction step: now I am stuck here how to process at step-1 'set up brain mask' ?

step-2: I just selected DSI and kept other things by default > Run reconstruction, this gives .fib file.

4). Also, how we do eddy current correction (and other preprocessing steps) and registration with structural/functional data ?

I would greatly appreciate any help.

Thanks,

Sahil

[Fang-Cheng Yeh]

Hi Sahil,

    I would recommend you use DICOM files in "STEP1". You may select all DICOM files and create an SRC. DSI Studio can get b-table from the DICOM headers. If nii file works for you, then it is still okay to use nii for creating src file.

   The brain mask page will give you a default mask. If the coverage seems good, then you don't have to change the mask. 

    The eddy current correction is not good for high b-value setting. It is good for DTI, but not DSI. My past experience with eddy current correction on DSI gives even worse result, and I personally won't recommend it. 

Best regards,

Frank

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[Sahil Bajaj]

Thank you so much Frank. This is really a very nice software. Thanks for that.

From here- http://dsi-studio.labsolver.org/Manual/Fiber-Tracking, I found definitions of almost all the parameters used during tracking but can you please tell me how to choose the best values of each parameter e.g. how do we know what length constraint or maximum number of fibers should we choose or what smoothing value, maximum angle, step size etc. should be chosen ?

Thanks a lot Frank.

Sahil

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Sahil Bajaj
Graduate Student
Neuroscience Research Group
Department of Physics & Astronomy

Georgia State University
Atlanta, GA, USA.
E-mail:sahil...@gmail.com

[Fang-Cheng Yeh]

Hi Sahil,

    The default values are the setting I suggested, but they should be modified for your cases. It depends on the trajectories of the fiber pathways you are to study. The prior information about the pathway determines the best setting.

    You may also take a look at the settings used by other studies  (under the citation list).

Best regards,

Frank