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replace thr by clip in eddy output, else we get a mask instead of a dwi
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@AlexVCaron
AlexVCaron committed Jul 23, 2024
1 parent 009e03c commit f8c9431
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Showing 3 changed files with 58 additions and 131 deletions.
2 changes: 1 addition & 1 deletion modules/nf-scil/preproc/eddy/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -93,7 +93,7 @@ process PREPROC_EDDY {
echo "--very_verbose $extra_args" >> eddy.sh
sh eddy.sh
scil_volume_math.py lower_threshold dwi_eddy_corrected.nii.gz 0 ${prefix}__dwi_corrected.nii.gz
scil_volume_math.py lower_clip dwi_eddy_corrected.nii.gz 0 ${prefix}__dwi_corrected.nii.gz
if [[ \$number_rev_dwi -eq 0 ]]
then
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3 changes: 2 additions & 1 deletion subworkflows/nf-scil/anatomical_segmentation/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,8 @@ workflow ANATOMICAL_SEGMENTATION {
ch_versions = Channel.empty()

// ** FSL fast segmentation ** //
SEGMENTATION_FASTSEG ( ch_image )
// TODO: Add lesion mask
SEGMENTATION_FASTSEG ( ch_image.map{ it + [""] } )
ch_versions = ch_versions.mix(SEGMENTATION_FASTSEG.out.versions.first())

// ** Setting outputs ** //
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184 changes: 55 additions & 129 deletions subworkflows/nf-scil/tractoflow/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -8,9 +8,9 @@
"id": "test",
"single_end": false
},
"test_dwi_resampled.nii.gz:md5,6db9e5b9e0cda99717ac7e32a797862c",
"test_dwi_resampled.nii.gz:md5,c9cbd6494df9e42abcdc7e5cfcbf828c",
"test__bval_eddy:md5,7995daabbd74fcf7c365a39a779f67e9",
"test__dwi_eddy_corrected.bvec:md5,3544093830861901af949343f69e7a10"
"test__dwi_eddy_corrected.bvec:md5,b1c4e58303885b66d6b267aa13571f5b"
]
],
"1": [
Expand All @@ -23,26 +23,15 @@
]
],
"10": [
[
{
"id": "test",
"single_end": false
},
"test__local_tracking.trk:md5,509d71fccb26821e65789240fe8414fd",
"test__local_tracking_config.json:md5,a278ccc2af912b62c0c4ecabff20db1f"
]

],
"11": [

],
"12": [
"versions.yml:md5,3a3c674e9221f19ed409a1890bc2eb39",
"versions.yml:md5,402c3604be37f571df13f983b1b5dd68",
"versions.yml:md5,689514aa26a4f84f83063f34c0e38190",
"versions.yml:md5,a3d1c964db9fa1079b738398a64219f7",
"versions.yml:md5,a986b4e17262e999e378666d281e9ef3",
"versions.yml:md5,ad06aa4db03ace5de5712b3fa021bf89",
"versions.yml:md5,b365d463ddf58fc7b47cd51c70876a11",
"versions.yml:md5,ba57313cd97586c885868a3aef7314a3",
"versions.yml:md5,fc6a2d3923b6ecd60b833ce5f09f8877"
],
Expand All @@ -52,7 +41,7 @@
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,310171fa6f46f5d32a9ff904592b65f4"
"test__t1_warped.nii.gz:md5,7dd7bd555aafd6d6483e5e5509a6b6bc"
]
],
"3": [
Expand All @@ -61,22 +50,14 @@
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,0edcb8ad87b53d83d4fe410247cc6c1f",
"test__output0GenericAffine.mat:md5,4030a29e7c4a4aec3a893ea2feda59e3",
"test__output0GenericAffine.mat:md5,4030a29e7c4a4aec3a893ea2feda59e3",
"test__output1InverseWarp.nii.gz:md5,217d7238692c049c4fb63d04ef868c06"
"test__output1Warp.nii.gz:md5,b4c0e54d52f84719157f934bd1894d34",
"test__output0GenericAffine.mat:md5,bb393dcf47cb64695fccc3b989593e10",
"test__output0GenericAffine.mat:md5,bb393dcf47cb64695fccc3b989593e10",
"test__output1InverseWarp.nii.gz:md5,cda5cb395702d69d2515eb23d21d4337"
]
],
"4": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,100b4de46ddf5828da7459c5e724feef",
"test__mask_gm.nii.gz:md5,7a2f778efbfd08e0de332bd765649d4b",
"test__mask_csf.nii.gz:md5,25b8c11928a2feab71900f2d4cc5de12"
]

],
"5": [

Expand All @@ -87,7 +68,7 @@
"id": "test",
"single_end": false
},
"test__tensor.nii.gz:md5,7b670547328c2f53b9d5b5e5b96ca521"
"test__tensor.nii.gz:md5,70acf24a5221bb3035489cd0c6804754"
]
],
"7": [
Expand All @@ -96,47 +77,29 @@
"id": "test",
"single_end": false
},
"test__ad.nii.gz:md5,11c162fc83f9b3ea4cdeb9220906d706",
"test__rd.nii.gz:md5,ec74fd816e198af0953c638aa184b6fc",
"test__md.nii.gz:md5,7da8aae4115c5cd18eaa2719f5343c1a",
"test__fa.nii.gz:md5,311956c30a0eda6ba18481d69a9f2f77",
"test__ga.nii.gz:md5,da60890c479602bd9f1c913e16f38800",
"test__rgb.nii.gz:md5,d77c33aeb865130636e56c5b16a70c87",
"test__evecs_v1.nii.gz:md5,aed7b0de70f3c374aed914cdbf78dc54",
"test__evecs_v2.nii.gz:md5,eaede582b120ed48ac66b3fdd65bdb87",
"test__evecs_v3.nii.gz:md5,b07308487465f13efc7528d7dfd77672",
"test__evals_e1.nii.gz:md5,11c162fc83f9b3ea4cdeb9220906d706",
"test__evals_e2.nii.gz:md5,14f855488ec6800a84d6336740b7a10d",
"test__evals_e3.nii.gz:md5,8e9eec05cd1d86b9b40ebdf68ab2c841",
"test__residual.nii.gz:md5,77d8ea73ef9506750b31c6bc5ad2c4f7",
"test__ad.nii.gz:md5,9b0a94a606b2f905cea541da14cc4b31",
"test__rd.nii.gz:md5,eafd81c8f57fe192d981c991303297b1",
"test__md.nii.gz:md5,04bd3997273a1469f9b847a61a5704f8",
"test__fa.nii.gz:md5,e99a8363a6bb7dbe786a176dccf3118c",
"test__ga.nii.gz:md5,798fb5e848824aa7808f59c6cf6ac5eb",
"test__rgb.nii.gz:md5,10eae95841a5d0e675f1d8c91a1dcc79",
"test__evecs_v1.nii.gz:md5,d1e2bf1db0f37886595ab0c1a6aeda20",
"test__evecs_v2.nii.gz:md5,2416618f6c952c0bf22fc66508a07b84",
"test__evecs_v3.nii.gz:md5,ef758b5da72652ea195a8a1be3836b20",
"test__evals_e1.nii.gz:md5,9b0a94a606b2f905cea541da14cc4b31",
"test__evals_e2.nii.gz:md5,a9dd902d19da24826e9719437be7779e",
"test__evals_e3.nii.gz:md5,6af6733f2bea6f93aefd5b7e11a446e5",
"test__residual.nii.gz:md5,ec5be059884f53d000e395c52781e2bb",
"test__nonphysical.nii.gz:md5,f4b5b404b0e5275fcb269f0e18d2d344",
"test__mode.nii.gz:md5,c959f553163c9258971726fadb94cedc",
"test__norm.nii.gz:md5,1f1c9135f82fdd86190e4118a7848f7b"
"test__mode.nii.gz:md5,ccb386d99394a03f8648c949759d2e27",
"test__norm.nii.gz:md5,0abb675167529634edd35e3b576d1884"
]
],
"8": [
[
{
"id": "test",
"single_end": false
},
"test__frf.txt:md5,f7a4f04e590b9e124382e0ac3ce83d96",
[

],
[

]
]

],
"9": [
[
{
"id": "test",
"single_end": false
},
"test__fodf.nii.gz:md5,25394d554892205115c5dd1a66cff63b"
]

],
"brain_mask": [
[
Expand All @@ -153,22 +116,22 @@
"id": "test",
"single_end": false
},
"test__ad.nii.gz:md5,11c162fc83f9b3ea4cdeb9220906d706",
"test__rd.nii.gz:md5,ec74fd816e198af0953c638aa184b6fc",
"test__md.nii.gz:md5,7da8aae4115c5cd18eaa2719f5343c1a",
"test__fa.nii.gz:md5,311956c30a0eda6ba18481d69a9f2f77",
"test__ga.nii.gz:md5,da60890c479602bd9f1c913e16f38800",
"test__rgb.nii.gz:md5,d77c33aeb865130636e56c5b16a70c87",
"test__evecs_v1.nii.gz:md5,aed7b0de70f3c374aed914cdbf78dc54",
"test__evecs_v2.nii.gz:md5,eaede582b120ed48ac66b3fdd65bdb87",
"test__evecs_v3.nii.gz:md5,b07308487465f13efc7528d7dfd77672",
"test__evals_e1.nii.gz:md5,11c162fc83f9b3ea4cdeb9220906d706",
"test__evals_e2.nii.gz:md5,14f855488ec6800a84d6336740b7a10d",
"test__evals_e3.nii.gz:md5,8e9eec05cd1d86b9b40ebdf68ab2c841",
"test__residual.nii.gz:md5,77d8ea73ef9506750b31c6bc5ad2c4f7",
"test__ad.nii.gz:md5,9b0a94a606b2f905cea541da14cc4b31",
"test__rd.nii.gz:md5,eafd81c8f57fe192d981c991303297b1",
"test__md.nii.gz:md5,04bd3997273a1469f9b847a61a5704f8",
"test__fa.nii.gz:md5,e99a8363a6bb7dbe786a176dccf3118c",
"test__ga.nii.gz:md5,798fb5e848824aa7808f59c6cf6ac5eb",
"test__rgb.nii.gz:md5,10eae95841a5d0e675f1d8c91a1dcc79",
"test__evecs_v1.nii.gz:md5,d1e2bf1db0f37886595ab0c1a6aeda20",
"test__evecs_v2.nii.gz:md5,2416618f6c952c0bf22fc66508a07b84",
"test__evecs_v3.nii.gz:md5,ef758b5da72652ea195a8a1be3836b20",
"test__evals_e1.nii.gz:md5,9b0a94a606b2f905cea541da14cc4b31",
"test__evals_e2.nii.gz:md5,a9dd902d19da24826e9719437be7779e",
"test__evals_e3.nii.gz:md5,6af6733f2bea6f93aefd5b7e11a446e5",
"test__residual.nii.gz:md5,ec5be059884f53d000e395c52781e2bb",
"test__nonphysical.nii.gz:md5,f4b5b404b0e5275fcb269f0e18d2d344",
"test__mode.nii.gz:md5,c959f553163c9258971726fadb94cedc",
"test__norm.nii.gz:md5,1f1c9135f82fdd86190e4118a7848f7b"
"test__mode.nii.gz:md5,ccb386d99394a03f8648c949759d2e27",
"test__norm.nii.gz:md5,0abb675167529634edd35e3b576d1884"
]
],
"dti_tensor": [
Expand All @@ -177,7 +140,7 @@
"id": "test",
"single_end": false
},
"test__tensor.nii.gz:md5,7b670547328c2f53b9d5b5e5b96ca521"
"test__tensor.nii.gz:md5,70acf24a5221bb3035489cd0c6804754"
]
],
"dwi": [
Expand All @@ -186,44 +149,19 @@
"id": "test",
"single_end": false
},
"test_dwi_resampled.nii.gz:md5,6db9e5b9e0cda99717ac7e32a797862c",
"test_dwi_resampled.nii.gz:md5,c9cbd6494df9e42abcdc7e5cfcbf828c",
"test__bval_eddy:md5,7995daabbd74fcf7c365a39a779f67e9",
"test__dwi_eddy_corrected.bvec:md5,3544093830861901af949343f69e7a10"
"test__dwi_eddy_corrected.bvec:md5,b1c4e58303885b66d6b267aa13571f5b"
]
],
"fodf": [
[
{
"id": "test",
"single_end": false
},
"test__fodf.nii.gz:md5,25394d554892205115c5dd1a66cff63b"
]

],
"frf": [
[
{
"id": "test",
"single_end": false
},
"test__frf.txt:md5,f7a4f04e590b9e124382e0ac3ce83d96",
[

],
[

]
]

],
"local_tractogram": [
[
{
"id": "test",
"single_end": false
},
"test__local_tracking.trk:md5,509d71fccb26821e65789240fe8414fd",
"test__local_tracking_config.json:md5,a278ccc2af912b62c0c4ecabff20db1f"
]

],
"pft_tractogram": [

Expand All @@ -234,7 +172,7 @@
"id": "test",
"single_end": false
},
"test__t1_warped.nii.gz:md5,310171fa6f46f5d32a9ff904592b65f4"
"test__t1_warped.nii.gz:md5,7dd7bd555aafd6d6483e5e5509a6b6bc"
]
],
"t1_to_b0_transformations": [
Expand All @@ -243,34 +181,22 @@
"id": "test",
"single_end": false
},
"test__output1Warp.nii.gz:md5,0edcb8ad87b53d83d4fe410247cc6c1f",
"test__output0GenericAffine.mat:md5,4030a29e7c4a4aec3a893ea2feda59e3",
"test__output0GenericAffine.mat:md5,4030a29e7c4a4aec3a893ea2feda59e3",
"test__output1InverseWarp.nii.gz:md5,217d7238692c049c4fb63d04ef868c06"
"test__output1Warp.nii.gz:md5,b4c0e54d52f84719157f934bd1894d34",
"test__output0GenericAffine.mat:md5,bb393dcf47cb64695fccc3b989593e10",
"test__output0GenericAffine.mat:md5,bb393dcf47cb64695fccc3b989593e10",
"test__output1InverseWarp.nii.gz:md5,cda5cb395702d69d2515eb23d21d4337"
]
],
"tissues_maps": [

],
"tissues_masks": [
[
{
"id": "test",
"single_end": false
},
"test__mask_wm.nii.gz:md5,100b4de46ddf5828da7459c5e724feef",
"test__mask_gm.nii.gz:md5,7a2f778efbfd08e0de332bd765649d4b",
"test__mask_csf.nii.gz:md5,25b8c11928a2feab71900f2d4cc5de12"
]

],
"versions": [
"versions.yml:md5,3a3c674e9221f19ed409a1890bc2eb39",
"versions.yml:md5,402c3604be37f571df13f983b1b5dd68",
"versions.yml:md5,689514aa26a4f84f83063f34c0e38190",
"versions.yml:md5,a3d1c964db9fa1079b738398a64219f7",
"versions.yml:md5,a986b4e17262e999e378666d281e9ef3",
"versions.yml:md5,ad06aa4db03ace5de5712b3fa021bf89",
"versions.yml:md5,b365d463ddf58fc7b47cd51c70876a11",
"versions.yml:md5,ba57313cd97586c885868a3aef7314a3",
"versions.yml:md5,fc6a2d3923b6ecd60b833ce5f09f8877"
]
Expand All @@ -280,6 +206,6 @@
"nf-test": "0.9.0-rc1",
"nextflow": "24.04.2"
},
"timestamp": "2024-07-05T02:09:28.140631"
"timestamp": "2024-07-23T14:39:42.244333"
}
}

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