Question Regarding TOPUP/EDDY Correction in DSI Studio

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Jaiprakash Gurav

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1:17 PM (4 hours ago) 1:17 PM
to DSI Studio

Dear Dr. Yeh,

I am currently working on a DTI dataset and am attempting to perform distortion correction using DSI Studio.

I have two DICOM image sets: one standard DTI acquisition and one reverse phase-encoding acquisition intended for TOPUP/EDDY correction. I imported the primary DTI series into the DSI Studio GUI and successfully generated an .sz file. However, when I navigate to the correction step and attempt to add the reverse phase-encoding dataset (either as a NIfTI file or as an .sz file), DSI Studio reports that I do not have permission to perform EDDY/TOPUP or no file.

I am using the GUI version of DSI Studio and am unsure whether this issue is related to missing dependencies, software permissions, or an installation/configuration problem. Could you please advise on how I should proceed? Specifically, are there additional requirements (such as FSL installation or configuration) that must be met before TOPUP/EDDY corrections can be executed through DSI Studio?

Thank you for your time and assistance.

Best regards,

Jaiprakash Gurav
Research Assistant III
Department of Neurosurgery
UTHealth Houston

Frank Yeh

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1:37 PM (4 hours ago) 1:37 PM
to jgu...@uth.edu, DSI Studio
Dear Jaiprakash,

Are you using the Windows or Mac version of DSI Studio?

If you are using Windows, the error is likely because the system is
blocking the "eddy.exe" file located in the DSI Studio plugin folder.
To resolve this, please navigate to that folder, manually click on the
"eddy.exe" file to run it, and select the option to allow your
computer to run the program. After then, DSI Studio should be able to
run eddy.

Best regards,
Frank
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Frank Yeh

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4:07 PM (1 hour ago) 4:07 PM
to Gurav, Jaiprakash S, DSI Studio
I uploaded DSI Studio.
Could you download the new version and see if it works?

If still not working please let me know.
Frank

On Mon, Jun 15, 2026, 13:56 Gurav, Jaiprakash S <Jaiprakas...@uth.tmc.edu> wrote:
This is the error I got 

┌──📟DSI Studio (Yeh 2025, doi:10.1038/s41592-025-02762-8), the Hou "侯" version (Jun 14 2026, http://dsi-studio.labsolver.org)
├──Enable multi-thread CPU computation 
├──┬──📟[Step T2][Reconstruction]
│  ├──┬──📂open /Volumes/Sector2/TA843B/TA843B_061226/DTI/20260612_F033Y_R-TA843B_R-TA843B_s2001.sz
│  │  ├──src ver: 202408 dim: 104 104 72 vs: 2.01923 2.01923 2 
│  │  ├──trans: -2.01923 0 0 207.981; 0 -2.01923 0 207.981; 0 0 2 0; 0 0 0 1;  dwi count: 105
│  │  ├──┬──📟reading data
│  │  │  └──⏱102ms
│  │  ├──┬──📟create mask from dwi sum
│  │  │  └──⏱354ms
│  │  └──⏱1s602ms
│  ├──change current directory to "/Volumes/Sector2/TA843B/TA843B_061226/DTI"
│  ├──┬──📟initiate interface
│  │  └──⏱3ms
│  └──⏱1s649ms
├──┬──📟[Step T2][Reconstruction]
│  ├──┬──📂open /Volumes/Sector2/TA843B/TA843B_061226/DTI/20260612_F033Y_R-TA843B_R-TA843B_s2001.sz
│  │  ├──src ver: 202408 dim: 104 104 72 vs: 2.01923 2.01923 2 
│  │  ├──trans: -2.01923 0 0 207.981; 0 -2.01923 0 207.981; 0 0 2 0; 0 0 0 1;  dwi count: 105
│  │  ├──┬──📟reading data
│  │  │  └──⏱85ms
│  │  ├──┬──📟create mask from dwi sum
│  │  │  └──⏱347ms
│  │  └──⏱1s519ms
│  ├──change current directory to "/Volumes/Sector2/TA843B/TA843B_061226/DTI"
│  ├──┬──📟initiate interface
│  │  └──⏱3ms
│  └──⏱1s557ms
├──┬──📟[Step T2][Corrections][TOPUP EDDY]
│  ├──param: /Volumes/Sector2/TA843B/TA843B_061226/DTI/DICOM/20260612_F033Y_R-TA843B_R-TA843B_s2101.sz
│  ├──┬──📂open /Volumes/Sector2/TA843B/TA843B_061226/DTI/DICOM/20260612_F033Y_R-TA843B_R-TA843B_s2101.sz
│  │  ├──src ver: 202408 dim: 104 104 72 vs: 2.01923 2.01923 2 
│  │  ├──trans: -2.01923 0 0 207.981; 0 -2.01923 0 207.981; 0 0 2 0; 0 0 0 1;  dwi count: 7
│  │  ├──┬──📟reading data
│  │  │  └──⏱9ms
│  │  ├──┬──📟create mask from dwi sum
│  │  │  └──⏱364ms
│  │  └──⏱463ms
│  ├──┬──📟run topup
│  │  ├──projected correction: 0.91921 0.998115 0 
│  │  ├──source com: 50.7895 49.7895 24.1053 
│  │  ├──rev pe com: 31.5 23.6667 35 
│  │  ├──source and reverse phase encoding: AP_PA
│  │  ├──create acq params at "/Volumes/Sector2/TA843B/TA843B_061226/DTI/20260612_F033Y_R-TA843B_R-TA843B_s2001.sz.topup.acqparams.txt"
│  │  ├──0 -1 0 0.05
│  │  ├──0 1 0 0.05
│  │  ├──create topup needed b0 nii.gz file from AP_PA b0
│  │  ├──┬──💾save /Volumes/Sector2/TA843B/TA843B_061226/DTI/20260612_F033Y_R-TA843B_R-TA843B_s2001.sz.topup.AP_PA.nii.gz
│  │  │  └──⏱702ms
│  │  ├──❗Cannot locate FSL: FSLDIR is not set. FSLDIR is a system environment variable that should point to your FSL install folder (e.g., /usr/local/fsl). Proceeding to call FSL tools via your PATH.
│  │  ├──run "topup"
│  │  ├──path: "/Volumes/Sector2/TA843B/TA843B_061226/DTI"
│  │  ├──--imain=20260612_F033Y_R-TA843B_R-TA843B_s2001.sz.topup.AP_PA.nii.gz
│  │  ├──--datain=20260612_F033Y_R-TA843B_R-TA843B_s2001.sz.topup.acqparams.txt
│  │  ├──--out=20260612_F033Y_R-TA843B_R-TA843B_s2001
│  │  ├──--iout=20260612_F033Y_R-TA843B_R-TA843B_s2001.sz.topup.check_result
│  │  ├──--verbose=1
│  │  ├──--warpres=20,16,14,12,10,6,4,4,4
│  │  ├──--subsamp=2,2,2,2,2,1,1,1,1
│  │  ├──--fwhm=8,6,4,3,3,2,1,0,0
│  │  ├──--miter=5,5,5,5,5,10,10,20,20
│  │  ├──--lambda=0.005,0.001,0.0001,0.000015,0.000005,0.0000005,0.00000005,0.0000000005,0.00000000001
│  │  ├──--ssqlambda=1
│  │  ├──--regmod=bending_energy
│  │  ├──--estmov=1,1,1,1,1,0,0,0,0
│  │  ├──--minmet=0,0,0,0,0,1,1,1,1
│  │  ├──--splineorder=3
│  │  ├──--numprec=double
│  │  ├──--interp=spline
│  │  ├──--scale=1
│  │  ├──❌topup failed to start. Either topup is missing, or you have no permission to run it.
│  │  └──⏱851ms
│  └──⏱1s324ms

From: Frank Yeh <fran...@gmail.com>
Sent: 15 June 2026 12:41
To: Gurav, Jaiprakash S <Jaiprakas...@uth.tmc.edu>
Subject: Re: [dsi-studio] Question Regarding TOPUP/EDDY Correction in DSI Studio
 
External: Increase caution when handling links and attachments.


Could you click on the "console" button of DSI Studio and post the
complete message?
I will check to see if there is a solution.
Frank

On Mon, Jun 15, 2026 at 1:38 PM Gurav, Jaiprakash S
<Jaiprakas...@uth.tmc.edu> wrote:
>
> Thank you Dr Yeh for replying I am using on Mac OS (intel)
>
> Best Regards
> JP
> ________________________________
> From: Frank Yeh <fran...@gmail.com>
> Sent: 15 June 2026 12:36
> To: jgu...@uth.edu <jgu...@uth.edu>
> Cc: DSI Studio <dsi-s...@googlegroups.com>
> Subject: Re: [dsi-studio] Question Regarding TOPUP/EDDY Correction in DSI Studio
>
> External: Increase caution when handling links and attachments.
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