From 75b6551ca6566d3b1d9b19f657d04b3328c4cd4f Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 15:12:12 +0000 Subject: [PATCH 1/5] change mrtrix to scilpy --- modules/nf-neuro/betcrop/antsbet/main.nf | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf index 04e51c10..774d70f2 100644 --- a/modules/nf-neuro/betcrop/antsbet/main.nf +++ b/modules/nf-neuro/betcrop/antsbet/main.nf @@ -34,7 +34,8 @@ process BETCROP_ANTSBET { -e $template -m $tissues_probabilities ${args.join(' ')} scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \ ${prefix}__t1_bet_mask.nii.gz --data_type uint8 - mrcalc $t1 ${prefix}__t1_bet_mask.nii.gz -mult ${prefix}__t1_bet.nii.gz -nthreads $task.cpus + scil_volume_math.py multiplication t1 ${prefix}__t1_bet_mask.nii.gz \ + ${prefix}__t1_bet.nii.gz --data_type float32 cat <<-END_VERSIONS > versions.yml "${task.process}": From f9983b5ed280afe940b5211d349a1f09b8256df9 Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 15:14:15 +0000 Subject: [PATCH 2/5] remove mrtrix version --- modules/nf-neuro/betcrop/antsbet/main.nf | 2 -- 1 file changed, 2 deletions(-) diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf index 774d70f2..42e9462e 100644 --- a/modules/nf-neuro/betcrop/antsbet/main.nf +++ b/modules/nf-neuro/betcrop/antsbet/main.nf @@ -40,7 +40,6 @@ process BETCROP_ANTSBET { cat <<-END_VERSIONS > versions.yml "${task.process}": scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/') END_VERSIONS """ @@ -60,7 +59,6 @@ process BETCROP_ANTSBET { cat <<-END_VERSIONS > versions.yml "${task.process}": scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2) - mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p') ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/') END_VERSIONS """ From 3c104661dfd34870dbca2e806bbe681b32fe6f00 Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 15:16:04 +0000 Subject: [PATCH 3/5] remove mrtrix help --- modules/nf-neuro/betcrop/antsbet/main.nf | 1 - 1 file changed, 1 deletion(-) diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf index 42e9462e..542cbd63 100644 --- a/modules/nf-neuro/betcrop/antsbet/main.nf +++ b/modules/nf-neuro/betcrop/antsbet/main.nf @@ -51,7 +51,6 @@ process BETCROP_ANTSBET { """ antsBrainExtraction.sh -h scil_volume_math.py -h - mrcalc -h touch ${prefix}__t1_bet.nii.gz touch ${prefix}__t1_bet_mask.nii.gz From 1ce4ae4b6ae2881e7fa0d9c42233d19f962f175b Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 16:07:34 +0000 Subject: [PATCH 4/5] update snaptest --- modules/nf-neuro/betcrop/antsbet/main.nf | 2 +- .../nf-neuro/betcrop/antsbet/tests/main.nf.test.snap | 12 ++++++------ .../nf-neuro/preproc_t1/tests/main.nf.test.snap | 8 ++++---- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf index 542cbd63..f9a78392 100644 --- a/modules/nf-neuro/betcrop/antsbet/main.nf +++ b/modules/nf-neuro/betcrop/antsbet/main.nf @@ -34,7 +34,7 @@ process BETCROP_ANTSBET { -e $template -m $tissues_probabilities ${args.join(' ')} scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \ ${prefix}__t1_bet_mask.nii.gz --data_type uint8 - scil_volume_math.py multiplication t1 ${prefix}__t1_bet_mask.nii.gz \ + scil_volume_math.py multiplication $t1 ${prefix}__t1_bet_mask.nii.gz \ ${prefix}__t1_bet.nii.gz --data_type float32 cat <<-END_VERSIONS > versions.yml diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap index 13625be9..f26a8e62 100644 --- a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap +++ b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap @@ -7,7 +7,7 @@ { "id": "test" }, - "test__t1_bet.nii.gz:md5,bd666c4ce559eab93690131f8b2a9101" + "test__t1_bet.nii.gz:md5,4fc936b6eeb1396e2537c2ec401d89ff" ] ], "1": [ @@ -19,7 +19,7 @@ ] ], "2": [ - "versions.yml:md5,9fde1445bc10857db69e440781e58cb7" + "versions.yml:md5,bb378e913d4002d0b644d3277892ae20" ], "mask": [ [ @@ -34,18 +34,18 @@ { "id": "test" }, - "test__t1_bet.nii.gz:md5,bd666c4ce559eab93690131f8b2a9101" + "test__t1_bet.nii.gz:md5,4fc936b6eeb1396e2537c2ec401d89ff" ] ], "versions": [ - "versions.yml:md5,9fde1445bc10857db69e440781e58cb7" + "versions.yml:md5,bb378e913d4002d0b644d3277892ae20" ] } ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.10.0" }, - "timestamp": "2024-10-30T17:42:18.337235926" + "timestamp": "2024-12-12T15:46:45.836683711" } } \ No newline at end of file diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap index 7f595ab8..d009322f 100644 --- a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap +++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap @@ -43,18 +43,18 @@ "test_cropped.nii.gz", "test_t1_cropped.nii.gz", [ - "versions.yml:md5,19aaa24cf046e49a4ad4ce5d507ea8aa", "versions.yml:md5,37229cd5cee6f6788fbc9083d6618c61", "versions.yml:md5,657fbb224f260392e573b8511c4b798d", "versions.yml:md5,b979132991d8f72a3585465533bd5730", "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740", + "versions.yml:md5,da278daafbe3afa8454021e2716dd205", "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea" ] ], "meta": { - "nf-test": "0.9.2", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.10.0" }, - "timestamp": "2024-12-04T10:38:12.185789" + "timestamp": "2024-12-12T15:50:29.838128539" } } \ No newline at end of file From f0ac51cc9309f0987a4ac7598310c41aa3662023 Mon Sep 17 00:00:00 2001 From: medde Date: Thu, 12 Dec 2024 16:17:31 +0000 Subject: [PATCH 5/5] remove mrtrix from metadata --- modules/nf-neuro/betcrop/antsbet/meta.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/modules/nf-neuro/betcrop/antsbet/meta.yml b/modules/nf-neuro/betcrop/antsbet/meta.yml index 4ce03b15..e85bfcb3 100644 --- a/modules/nf-neuro/betcrop/antsbet/meta.yml +++ b/modules/nf-neuro/betcrop/antsbet/meta.yml @@ -10,9 +10,6 @@ tools: - "scilpy": description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox." homepage: "https://github.com/scilus/scilpy.git" - - "MRtrix3": - description: "Toolbox for image processing, analysis and visualisation of dMRI." - homepage: "https://mrtrix.readthedocs.io/en/latest/" - "ants": description: "Advanced Normalization Tools." homepage: "https://github.com/ANTsX/ANTs"