Skip to content

[WIP] Update preQC #34

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
EliseCos wants to merge 2 commits into
base: main
Choose a base branch
from
Open

[WIP] Update preQC #34

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
2 commits
Select commit Hold shift + click to select a range
44c1cc4
add ideal bvalue
EliseCos Dec 13, 2025
13e7b44
Add a note about the first execution time
EliseCos Dec 13, 2025
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
1 change: 1 addition & 0 deletions main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -57,6 +57,7 @@ workflow get_data {

workflow {

log.warn('During the first execution, nf-mouse may take some time to download the necessary modules.')
log.info("Uses GPU: $params.use_gpu")
// Define channel for multiqc files
ch_multiqc_files = Channel.empty()
Expand Down
8 changes: 4 additions & 4 deletions modules/local/mouse/preqc/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -20,12 +20,16 @@ process PRE_QC {
script:
def prefix = task.ext.prefix ?: "${meta.id}"
def b0_threshold = task.ext.b0_thr_extract_b0 ? "--b0_threshold $task.ext.b0_thr_extract_b0" : ""
def threshold = task.ext.b0_thr_extract_b0 ? "$task.ext.b0_thr_extract_b0" : ""

"""
echo "This module is highly experimental"
echo "Be careful with the output."
echo ""

# Fetch b-values.
awk -v thr=${threshold} '{for(i=1;i<=NF;i++) if(\$i < thr) \$i=0.0; else \$i=int(\$i*10+(\$i>=0?0.5:-0.5))/10; print}' $bval > ${prefix}__stride_dwi.bval

# Fetch strides.
strides=\$(mrinfo $dwi -strides)
# Compare strides
Expand All @@ -36,7 +40,6 @@ process PRE_QC {

mrconvert $dwi ${prefix}__stride_dwi.nii.gz -strides 1,2,3,4
scil_gradients_modify_axes.py $bvec ${prefix}__stride_dwi.bvec -1 2 3
cp $bval ${prefix}__stride_dwi.bval

elif [ "\$strides" == "1 -2 3 4" ]; then
echo "Strides are not (1,2,3,4), converting to 1,2,3,4."
Expand All @@ -45,17 +48,14 @@ process PRE_QC {

mrconvert $dwi ${prefix}__stride_dwi.nii.gz -strides 1,2,3,4
cp $bvec ${prefix}__stride_dwi.bvec
cp $bval ${prefix}__stride_dwi.bval

elif [ "\$strides" == "1 2 3 4" ]; then
echo "Strides are already 1,2,3,4"
cp $dwi ${prefix}__stride_dwi.nii.gz
cp $bval ${prefix}__stride_dwi.bval
cp $bvec ${prefix}__stride_dwi.bvec
else
echo "Strides are: \$strides"
echo "There is no automatic way to transform to 1,2,3,4."
cp $bval ${prefix}__stride_dwi.bval
cp $bvec ${prefix}__stride_dwi.bvec
fi

Expand Down