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[EmmaRenauld]

I my case, I ran tractoflow with: run_denoise_dwi false, topup false, eddy false. I still had the Bet on the DWI.

During QC, however, the QC_Brain_Extraction_DWI does not run. I checked why. It uses dwi_mask_for_bet, which comes from dwi_eddy_for_bet, which is created with:

Channel
    .fromPath(["$input/**/Eddy/*dwi_corrected.nii.gz", "$input/**/Eddy_Topup/*dwi_corrected.nii.gz"], maxDepth:3)
    .collect(sort:true)
    .map{[it]}
    .set{dwi_eddy_for_bet}

But I have none of these files.

[EmmaRenauld]

Just so you know. To fix this for me, I added a symlink in my tractoflow output: a folder named Input pointing to my input.

Then in the main.nf, I changed line 78 to get dwi_eddy_for_bet from $input/**/Input/dwi.nii.gz.