From 793ff1b7877d1ffb5cdae69c5f6568d485aeb0e3 Mon Sep 17 00:00:00 2001 From: arnaudbore Date: Thu, 21 Nov 2024 21:46:47 +0000 Subject: [PATCH 1/2] answer issue 41 --- modules/nf-neuro/betcrop/cropvolume/main.nf | 5 +++++ modules/nf-neuro/preproc/n4/main.nf | 2 +- 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/modules/nf-neuro/betcrop/cropvolume/main.nf b/modules/nf-neuro/betcrop/cropvolume/main.nf index 8f4072d..82ce329 100755 --- a/modules/nf-neuro/betcrop/cropvolume/main.nf +++ b/modules/nf-neuro/betcrop/cropvolume/main.nf @@ -43,6 +43,11 @@ process BETCROP_CROPVOLUME { touch ${prefix}_${suffix}.nii.gz + if task.ext.output_bbox + do + touch ${prefix}_${suffix}_bbox.pkl + done + cat <<-END_VERSIONS > versions.yml "${task.process}": scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) diff --git a/modules/nf-neuro/preproc/n4/main.nf b/modules/nf-neuro/preproc/n4/main.nf index 5e02fd0..d3d03d6 100644 --- a/modules/nf-neuro/preproc/n4/main.nf +++ b/modules/nf-neuro/preproc/n4/main.nf @@ -59,7 +59,7 @@ process PREPROC_N4 { def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ - N4BiasFieldCorrection.py -h + N4BiasFieldCorrection -h scil_dwi_apply_bias_field -h touch ${prefix}__image_n4.nii.gz From 18273a2cef9ffdaf7088e305b9c4ebf4dd439079 Mon Sep 17 00:00:00 2001 From: Arnaud Bore Date: Thu, 21 Nov 2024 17:15:14 -0500 Subject: [PATCH 2/2] Update modules/nf-neuro/preproc/n4/main.nf Co-authored-by: Alex Valcourt Caron --- modules/nf-neuro/preproc/n4/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nf-neuro/preproc/n4/main.nf b/modules/nf-neuro/preproc/n4/main.nf index d3d03d6..446ca5c 100644 --- a/modules/nf-neuro/preproc/n4/main.nf +++ b/modules/nf-neuro/preproc/n4/main.nf @@ -60,7 +60,7 @@ process PREPROC_N4 { def prefix = task.ext.prefix ?: "${meta.id}" """ N4BiasFieldCorrection -h - scil_dwi_apply_bias_field -h + scil_dwi_apply_bias_field.py -h touch ${prefix}__image_n4.nii.gz