Eddy correction does not work on Mac

[Eleonora Grande]

In step T2 reconstruction, when selecting eddy in the correction menu this is the output 

[Step T2][Corrections][EDDY]

│ ├──cannot find topup result: /Users/nf2/Desktop/data/217/217_Funzionale_2025_20250610104906_7_fieldcoef.nii.gz

│ ├──run eddy without topup

│ ├──┬──📟prepare file for tupup/eddy

│ │ ├──💾save temporary nifti file at /Users/nf2/Desktop/data/217/217_Funzionale_2025_20250610104906_7.sz.nii.gz

│ │ └──⏱6.689s

│ ├──┬──📟run eddy

│ │ ├──FSL installation not found: cannot find environmental variable FSLDIR, try calling directly

│ │ ├──run eddy

│ │ ├──path: /Users/nf2/Desktop/data/217

│ │ ├──--imain=217_Funzionale_2025_20250610104906_7.sz.nii.gz

│ │ ├──--mask=217_Funzionale_2025_20250610104906_7.sz.mask.nii.gz

│ │ ├──--acqp=217_Funzionale_2025_20250610104906_7.sz.topup.acqparams.txt

│ │ ├──--index=217_Funzionale_2025_20250610104906_7.sz.index.txt

│ │ ├──--bvecs=217_Funzionale_2025_20250610104906_7.sz.bvec

│ │ ├──--bvals=217_Funzionale_2025_20250610104906_7.sz.bval

│ │ ├──--out=217_Funzionale_2025_20250610104906_7.sz.corrected

│ │ ├──--verbose=1

│ │ ├──❌eddy failed to start. Either eddy is missing, or you have no permission to run it.

│ │ └──⏱17ms

any suggestion? Thanks

[Frank Yeh]

You may need to install FSL to run Eddy correction.

Best regards

Frank

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[Eleonora Grande]

Already installed!

[Frank Yeh]

The message showed " cannot find environmental variable FSLDIR " You may need to set up the variable pointing to the FSL installation path.

Best regards,

Frank

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[Eleonora Grande]

Thank you so much for your help! How can I do that?

Best regards,

Eleonora

[DSI Studio]

Here is chatgpt answer:

To set FSLDIR in macOS so that it points to your FSL installation path, follow these steps:

---

🔧 Step 1: Locate your FSL installation

If you used Homebrew, the path is likely:

/opt/homebrew/opt/fsl

Or, if installed manually (e.g., from fsl.fmrib.ox.ac.uk), it might be:

/Users/yourname/fsl

---

📄 Step 2: Edit your shell profile

Depending on the shell you're using, edit the appropriate file:

• For zsh (default in macOS Catalina and later):

  nano ~/.zshrc

• For bash:

  nano ~/.bash_profile

---

⚙️ Step 3: Add the following lines export FSLDIR=/path/to/your/fsl source $FSLDIR/etc/fslconf/fsl.sh export PATH=$FSLDIR/bin:$PATH

🔁 Replace /path/to/your/fsl with your actual FSL directory, e.g.:

export FSLDIR=/opt/homebrew/opt/fsl source $FSLDIR/etc/fslconf/fsl.sh export PATH=$FSLDIR/bin:$PATH

---

✅ Step 4: Apply the changes

After saving the file, run:

source ~/.zshrc # or ~/.bash_profile

You can confirm it's working with:

echo $FSLDIR which fsl

Let me know if you're using Homebrew or a manual install — I can give more tailored help if needed!

[Eleonora Grande]

Thank you for your help! I tried but still getting error..

[DSI Studio]

Did you follows chatgpt's steps? What error message did you get?