Skip to content

Update fw noddi #329

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

Merged
arnaudbore merged 2 commits into from
Feb 27, 2026
Merged

Update fw noddi #329

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
1cc9ba0
Update freewater, noddi and diffusivitypriors
levje Feb 27, 2026
a60474c
Merge branch 'main' into update-fw-noddi
levje Feb 27, 2026
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
2 changes: 1 addition & 1 deletion modules/nf-neuro/reconst/diffusivitypriors/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process RECONST_DIFFUSIVITYPRIORS {
tag "$meta.id"
label 'process_single'

container "scilus/scilpy:dev" // TODO: Replace this container with an official one once available.
container "scilus/scilpy:2.2.2_cpu"

input:
tuple val(meta), path(fa), path(ad), path(rd), path(md)
Expand Down
12 changes: 6 additions & 6 deletions modules/nf-neuro/reconst/diffusivitypriors/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,25 +137,25 @@
]
],
[
"versions.yml:md5,81f780d3d557fd27e4724ea81fbe6f1a"
"versions.yml:md5,9614f69f1fd8319213a31140c654ed84"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.6"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-14T15:18:34.825370539"
"timestamp": "2026-02-26T23:05:20.206018637"
},
"reconst - diffusivitypriors - stub-run": {
"content": [
[
"versions.yml:md5,81f780d3d557fd27e4724ea81fbe6f1a"
"versions.yml:md5,9614f69f1fd8319213a31140c654ed84"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.6"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-14T15:18:39.245577816"
"timestamp": "2026-02-26T23:05:24.880867377"
}
}
7 changes: 6 additions & 1 deletion modules/nf-neuro/reconst/freewater/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ process RECONST_FREEWATER {
tag "$meta.id"
label 'process_low'

container "scilus/scilpy:2.2.0_cpu"
container "scilus/scilpy:2.2.2_cpu"

input:
tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(kernels), val(para_diff), val(iso_diff), val(perp_diff_min), val(perp_diff_max)
Expand Down Expand Up @@ -65,6 +65,11 @@ process RECONST_FREEWATER {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
# Set home directory. This is problematic if the container is run
# with non-root user which does not create a home directory, whilst
# AMICO attempts to write in the home directory, raising an error.
export HOME=/tmp

scil_freewater_maps -h
mkdir kernels
touch "${prefix}__dwi_fw_corrected.nii.gz"
Expand Down
28 changes: 14 additions & 14 deletions modules/nf-neuro/reconst/freewater/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,32 +2,32 @@
"reconst - freewater - stub-run": {
"content": [
[
"versions.yml:md5,b7348842aae4271b2d6831f596bae6f3"
"versions.yml:md5,8655aa3f6156a402b21af91cf01c0ed4"
]
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-23T18:05:08.029531192"
"timestamp": "2026-02-26T23:24:39.878161525"
},
"reconst - freewater_no_mask_compute_only": {
"content": [
[
"versions.yml:md5,b7348842aae4271b2d6831f596bae6f3"
"versions.yml:md5,8655aa3f6156a402b21af91cf01c0ed4"
],
11
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "25.04.7"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-23T18:54:46.117963036"
"timestamp": "2026-02-26T23:11:42.042994441"
},
"reconst - freewater": {
"content": [
[
"versions.yml:md5,b7348842aae4271b2d6831f596bae6f3"
"versions.yml:md5,8655aa3f6156a402b21af91cf01c0ed4"
],
11,
"test__dwi_fw_corrected.nii.gz",
Expand All @@ -38,14 +38,14 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2026-01-06T21:48:42.006348"
"timestamp": "2026-02-26T23:07:11.489341481"
},
"reconst - freewater - with priors": {
"content": [
[
"versions.yml:md5,b7348842aae4271b2d6831f596bae6f3"
"versions.yml:md5,8655aa3f6156a402b21af91cf01c0ed4"
],
11,
"test__dwi_fw_corrected.nii.gz",
Expand All @@ -56,8 +56,8 @@
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2026-01-06T21:50:50.568852"
"timestamp": "2026-02-26T23:08:05.039059796"
}
}
7 changes: 6 additions & 1 deletion modules/nf-neuro/reconst/noddi/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@ process RECONST_NODDI {
tag "$meta.id"
label 'process_medium'

container "scilus/scilpy:2.2.0_cpu"
container "scilus/scilpy:2.2.2_cpu"

input:
tuple val(meta), path(dwi), path(bval), path(bvec), path(mask), path(kernels), val(para_diff), val(iso_diff)
Expand Down Expand Up @@ -87,6 +87,11 @@ process RECONST_NODDI {
def prefix = task.ext.prefix ?: "${meta.id}"

"""
# Set home directory. This is problematic if the container is run
# with non-root user which does not create a home directory, whilst
# AMICO attempts to write in the home directory, raising an error.
export HOME=/tmp

scil_NODDI_maps -h
scil_volume_math -h

Expand Down
24 changes: 12 additions & 12 deletions modules/nf-neuro/reconst/noddi/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,15 @@
"test__ecvf.nii.gz",
"test__odi.nii.gz",
[
"versions.yml:md5,3c8accc418234ecdbf36f805b000818c"
"versions.yml:md5,d52a676c51564a0311f5029ba67aaf29"
],
145
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2026-01-07T12:49:41.217264"
"timestamp": "2026-02-26T23:18:48.788717523"
},
"reconst - noddi - with priors": {
"content": [
Expand All @@ -25,39 +25,39 @@
"test__ecvf.nii.gz",
"test__odi.nii.gz",
[
"versions.yml:md5,3c8accc418234ecdbf36f805b000818c"
"versions.yml:md5,d52a676c51564a0311f5029ba67aaf29"
],
145
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.8"
"nextflow": "25.10.2"
},
"timestamp": "2026-01-07T12:52:14.874089"
"timestamp": "2026-02-26T23:19:46.00348974"
},
"reconst - noddi - save_kernels - no mask": {
"content": [
[
"versions.yml:md5,3c8accc418234ecdbf36f805b000818c"
"versions.yml:md5,d52a676c51564a0311f5029ba67aaf29"
],
145
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.6"
"nextflow": "25.10.2"
},
"timestamp": "2025-12-11T15:12:31.541942034"
"timestamp": "2026-02-26T23:17:51.450449021"
},
"reconst - noddi - stub-run": {
"content": [
[
"versions.yml:md5,3c8accc418234ecdbf36f805b000818c"
"versions.yml:md5,d52a676c51564a0311f5029ba67aaf29"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.04.6"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-13T16:58:51.218060667"
"timestamp": "2026-02-26T23:27:46.254323732"
}
}
58 changes: 29 additions & 29 deletions subworkflows/nf-neuro/reconst_fw_noddi/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -165,16 +165,16 @@
]
],
"versions": [
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0"
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:36:39.598881865"
"timestamp": "2026-02-26T23:29:23.820516886"
},
"reconst_fw_noddi - noddi & freewater - custom priors": {
"content": [
Expand Down Expand Up @@ -548,20 +548,20 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0"
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3",
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:36:07.605628754"
"timestamp": "2026-02-26T23:28:51.64962634"
},
"reconst_fw_noddi - noddi & freewater": {
"content": [
Expand Down Expand Up @@ -774,18 +774,18 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,70017630e95110c203240f3be07c716b",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,9fe765550b2a3f33e52de7bdd91daf0b"
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:35:40.018200469"
"timestamp": "2026-02-26T23:28:24.016168121"
},
"reconst_fw_noddi - noddi & freewater - average priors": {
"content": [
Expand Down Expand Up @@ -998,19 +998,19 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,21ec0c32bc11dca0c4ccc95fdf1a2690",
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,70017630e95110c203240f3be07c716b",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,9fe765550b2a3f33e52de7bdd91daf0b"
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:35:54.886878716"
"timestamp": "2026-02-26T23:28:38.89054199"
},
"reconst_fw_noddi - noddi": {
"content": [
Expand Down Expand Up @@ -1061,16 +1061,16 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,9fe765550b2a3f33e52de7bdd91daf0b"
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,70017630e95110c203240f3be07c716b"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:35:10.744721888"
"timestamp": "2026-02-26T23:27:55.253043493"
},
"reconst_fw_noddi - freewater": {
"content": [
Expand Down Expand Up @@ -1238,17 +1238,17 @@
]
],
"versions": [
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,70017630e95110c203240f3be07c716b",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,9fe765550b2a3f33e52de7bdd91daf0b"
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:35:25.549988741"
"timestamp": "2026-02-26T23:28:09.646051384"
},
"reconst_fw_noddi - noddi - custom priors": {
"content": [
Expand Down Expand Up @@ -1299,15 +1299,15 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95"
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:36:27.080369611"
"timestamp": "2026-02-26T23:29:11.365231081"
},
"reconst_fw_noddi - noddi & freewater - custom priors subject-bound": {
"content": [
Expand Down Expand Up @@ -1520,16 +1520,16 @@
]
],
"versions": [
"versions.yml:md5,0576c1fdab3c59610cd67015e8146f95",
"versions.yml:md5,689b2c4f00690ac95de93f6175661a17",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0"
"versions.yml:md5,62b008e3bc1925b77790071d9e96a1a2",
"versions.yml:md5,9afc90b08b74fc84e879e1d2d0d7c7d0",
"versions.yml:md5,d1764b00cbc88145b08362c8ae9762b3"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-02-26T15:36:20.35765599"
"timestamp": "2026-02-26T23:29:04.257198065"
}
}
Loading