DSI Studio Eddy Implementation

[Steven J Granger]

Hi,

I am working with a dwMRI scheme that has a larger number of samples/directions (n=65) at 3000 and n=15 samples at b=1000 and b=2000 and n=6 at b=500. 

DSI studio throws the following error at the eddy stage: cannot run eddy due to not enough average sampling in the shell

Can you advise on whether DSI studio can handle the -data_is_shelled option from eddy and how I can implement that here in the following: src and qsdr calls: 

main1=$(ls $path/*DTI_pe1_dwi.nii.gz)
main2=$(ls $path/*DTI_pe0_dwi.nii.gz)

fslroi $main2 $output/A2P_b0 0 1

dsi_studio --action=src --source=$main1 --output=$output --bvec=/data/bvec --bval=/data/bval

dsi_studio --action=rec --source=$output/*.sz --rev_pe=$output/A2P_b0.nii.gz --check_btable --motion_correction --method=4 --param0=1.25 --output=$output

Thank you in advance! Ultimately I am hoping to stick with DSI studio's eddy/topup to avoid computational demands of running this directly in fsl. any advice would be appreciated! 

Best,

Steve 

[Frank Yeh]

This is FSL eddy's constraint. FSL eddy won't be able to use the n=6 at b=500. 

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[Frank Yeh]

I updated DSI Studio to use --data_is_shelled and lift this restriction. The new build should be ready in one hour or two (MacOS).

Frank

[Steven J Granger]

Thank you Frank! 

I will be able to give this a try sometime tomorrow and will let you know how it goes. 

Best,

Steve 

--

Steven J. Granger | Graduate Student Researcher

Center for the Neurobiology of Learning and Memory

Department of Neurobiology and Behavior

University of California, Irvine

gran...@uci.edu 

[Frank Yeh]

Yes

On Wed, Feb 25, 2026 at 11:33 AM Steven J Granger <gran...@uci.edu> wrote:

Could I confirm the update would apply to the linux builds as well? 

[Steven J Granger]

Could I confirm the update would apply to the linux builds as well? 

[Steven J Granger]

great, thanks!!