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will have to open an issue for more options for eddy in scipy
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@AlexVCaron
AlexVCaron committed Jan 14, 2025
1 parent 52024ea commit 8c9a0d5
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Showing 5 changed files with 42 additions and 46 deletions.
5 changes: 2 additions & 3 deletions modules/nf-neuro/preproc/eddy/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -20,7 +20,6 @@ process PREPROC_EDDY {
task.ext.when == null || task.ext.when

script:
def eddy_options = task.ext.args ? "--eddy_options \"$task.ext.args\"" : ""
def prefix = task.ext.prefix ?: "${meta.id}"
def slice_drop_flag = task.ext.slice_drop_correction ? "--slice_drop_correction " : ""
def bet_topup_before_eddy_f = task.ext.bet_topup_before_eddy_f ?: ""
Expand Down Expand Up @@ -74,7 +73,7 @@ process PREPROC_EDDY {
--readout $readout --out_script --fix_seed\
--n_reverse \${number_rev_dwi}\
--lsr_resampling\
$slice_drop_flag $eddy_options
$slice_drop_flag
else
scil_dwi_extract_b0.py \${dwi} \${bval} \${bvec} ${prefix}__b0.nii.gz --mean\
--b0_threshold $b0_thr_extract_b0 --skip_b0_check
Expand All @@ -89,7 +88,7 @@ process PREPROC_EDDY {
--eddy_cmd $eddy_cmd --b0_thr $b0_thr_extract_b0\
--encoding_direction $encoding\
--readout $readout --out_script --fix_seed\
$slice_drop_flag $eddy_options
$slice_drop_flag
fi
echo "--very_verbose $extra_args" >> eddy.sh
Expand Down
1 change: 0 additions & 1 deletion subworkflows/nf-neuro/tractoflow/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -33,7 +33,6 @@ process {
ext.b0_thr_extract_b0 = params.dwi_b0_extract_threshold
ext.encoding = "y" //FIXME : this is subject bound, pass through meta ?
ext.readout = 0.062 //FIXME : this is subject bound, pass through meta ?
ext.args = params.dwi_motion_and_eddy_filter_command_args
}

withName: "TRACTOFLOW:PREPROC_DWI:BETCROP_FSLBETCROP" {
Expand Down
1 change: 0 additions & 1 deletion subworkflows/nf-neuro/tractoflow/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -30,7 +30,6 @@ params {
dwi_motion_and_eddy_filter_command = "eddy_cpu"
dwi_motion_and_eddy_filter_bet_f_threshold = 0.16
dwi_motion_and_eddy_filter_restore_slices = true
dwi_motion_and_eddy_filter_command_args = ""

//**Final DWI BET**//
dwi_mask_final_bet_f_threshold = 0.16
Expand Down
3 changes: 1 addition & 2 deletions subworkflows/nf-neuro/tractoflow/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -39,9 +39,8 @@ nextflow_workflow {
test("tractoflow - no rev") {
when {
params {
dwi_motion_and_eddy_filter_command_args = "--fep"
dwi_motion_and_eddy_filter_bet_f_threshold = 0.3
dwi_mask_final_bet_f_threshold = 0.3
dwi_mask_final_bet_f_threshold = 0.16
fodf_pft_fit_seeding_n_seeds = 1
fodf_pft_fit_filter_n_particles = 4
fodf_local_fit_seeding_n_seeds = 1
Expand Down
78 changes: 39 additions & 39 deletions subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -15,33 +15,33 @@
{
"id": "test"
},
"test__t1_warped.nii.gz:md5,8d02cdc310475e7d9f73ed7e61835f80"
"test__t1_warped.nii.gz:md5,e1d5080a5280df16a719c39825ce5ba2"
]
],
"10": [
[
{
"id": "test"
},
"test__output1Warp.nii.gz:md5,bab8ac8676cdca96f780eb1a93a254f2",
"test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88"
"test__output1Warp.nii.gz:md5,e4956aa73a6f497e5c316dfe24086fa9",
"test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237"
]
],
"11": [
[
{
"id": "test"
},
"test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88",
"test__output1InverseWarp.nii.gz:md5,74060775a192a4d051ee0dc26e309e65"
"test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237",
"test__output1InverseWarp.nii.gz:md5,532398bd5366613c4ceb71f09227a343"
]
],
"12": [
[
{
"id": "test"
},
"test_t1_cropped.nii.gz:md5,b31fd188e250502273f89c0c73c34628"
"test_t1_cropped.nii.gz:md5,c804e09ae12b053d76e10a3d74e98fb6"
]
],
"13": [
Expand Down Expand Up @@ -105,7 +105,7 @@
{
"id": "test"
},
"test__mask_wm.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__mask_wm.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"20": [
Expand Down Expand Up @@ -189,7 +189,7 @@
{
"id": "test"
},
"test__mask_gm.nii.gz:md5,444e4c93ed39418f015cca8711c7f3fc"
"test__mask_gm.nii.gz:md5,40756ebc4a82a284a170ad699e0a5e30"
]
],
"30": [
Expand Down Expand Up @@ -246,7 +246,7 @@
{
"id": "test"
},
"test__pft_tracking.trk:md5,9234bb8361568b22baebd47d050fcedf"
"test__pft_tracking.trk:md5,38b3f540d2f112d5bbf026416b3d27ec"
]
],
"39": [
Expand All @@ -262,39 +262,39 @@
{
"id": "test"
},
"test__mask_csf.nii.gz:md5,356b9cae3adb8579e17a8679a27117d3"
"test__mask_csf.nii.gz:md5,277db7da3c1ed92947c177edeb5eaa7d"
]
],
"40": [
[
{
"id": "test"
},
"test__map_include.nii.gz:md5,f6ab6cb53316ab7d4672230e20aa0ea8"
"test__map_include.nii.gz:md5,d9983cec6fe4dbc7becce71ffac237b8"
]
],
"41": [
[
{
"id": "test"
},
"test__map_exclude.nii.gz:md5,b41e6b0f1c5697856cba3669746e7b4d"
"test__map_exclude.nii.gz:md5,44839611fb77fd588e99b9afa0ae6b91"
]
],
"42": [
[
{
"id": "test"
},
"test__pft_seeding_mask.nii.gz:md5,1a824035733bd230eb82fd79c8ab6cdc"
"test__pft_seeding_mask.nii.gz:md5,3429293546e20469c84502394e37885d"
]
],
"43": [
[
{
"id": "test"
},
"test__local_tracking.trk:md5,53432f584dcceeaa4b95874905e21224"
"test__local_tracking.trk:md5,5bf9827570b27aa3eaf19f9d76bae764"
]
],
"44": [
Expand All @@ -310,15 +310,15 @@
{
"id": "test"
},
"test__local_seeding_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__local_seeding_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"46": [
[
{
"id": "test"
},
"test__local_tracking_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__local_tracking_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"47": [
Expand Down Expand Up @@ -350,7 +350,7 @@
{
"id": "test"
},
"test__map_wm.nii.gz:md5,c1fa90c2f2687dc206ee681a3420c525"
"test__map_wm.nii.gz:md5,cd10401b5feee8c2bc531b34612ac959"
]
],
"50": [
Expand Down Expand Up @@ -378,15 +378,15 @@
{
"id": "test"
},
"test__map_gm.nii.gz:md5,2fcc377353a21f697878d8e45b2dc2c1"
"test__map_gm.nii.gz:md5,9ea2161ff256ba6680db86c28624191a"
]
],
"7": [
[
{
"id": "test"
},
"test__map_csf.nii.gz:md5,9c5cc395eeaffd3ec7a7f9baa07122cc"
"test__map_csf.nii.gz:md5,68f53afcc61f09d70484665161415aa8"
]
],
"8": [
Expand Down Expand Up @@ -424,8 +424,8 @@
{
"id": "test"
},
"test__output1Warp.nii.gz:md5,bab8ac8676cdca96f780eb1a93a254f2",
"test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88"
"test__output1Warp.nii.gz:md5,e4956aa73a6f497e5c316dfe24086fa9",
"test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237"
]
],
"aparc_aseg": [
Expand All @@ -439,24 +439,24 @@
{
"id": "test"
},
"test__map_csf.nii.gz:md5,9c5cc395eeaffd3ec7a7f9baa07122cc"
"test__map_csf.nii.gz:md5,68f53afcc61f09d70484665161415aa8"
]
],
"csf_mask": [
[
{
"id": "test"
},
"test__mask_csf.nii.gz:md5,356b9cae3adb8579e17a8679a27117d3"
"test__mask_csf.nii.gz:md5,277db7da3c1ed92947c177edeb5eaa7d"
]
],
"diffusion_to_anatomical": [
[
{
"id": "test"
},
"test__output0GenericAffine.mat:md5,a8749c8f3e24dc98fa2299acf8076a88",
"test__output1InverseWarp.nii.gz:md5,74060775a192a4d051ee0dc26e309e65"
"test__output0GenericAffine.mat:md5,7ce31e1314d3f591b07eb5844e6cc237",
"test__output1InverseWarp.nii.gz:md5,532398bd5366613c4ceb71f09227a343"
]
],
"dti_ad": [
Expand Down Expand Up @@ -620,15 +620,15 @@
{
"id": "test"
},
"test__map_gm.nii.gz:md5,2fcc377353a21f697878d8e45b2dc2c1"
"test__map_gm.nii.gz:md5,9ea2161ff256ba6680db86c28624191a"
]
],
"gm_mask": [
[
{
"id": "test"
},
"test__mask_gm.nii.gz:md5,444e4c93ed39418f015cca8711c7f3fc"
"test__mask_gm.nii.gz:md5,40756ebc4a82a284a170ad699e0a5e30"
]
],
"local_config": [
Expand All @@ -644,23 +644,23 @@
{
"id": "test"
},
"test__local_seeding_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__local_seeding_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"local_tracking_mask": [
[
{
"id": "test"
},
"test__local_tracking_mask.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__local_tracking_mask.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"local_tractogram": [
[
{
"id": "test"
},
"test__local_tracking.trk:md5,53432f584dcceeaa4b95874905e21224"
"test__local_tracking.trk:md5,5bf9827570b27aa3eaf19f9d76bae764"
]
],
"nonphysical_voxels": [
Expand Down Expand Up @@ -692,31 +692,31 @@
{
"id": "test"
},
"test__map_exclude.nii.gz:md5,b41e6b0f1c5697856cba3669746e7b4d"
"test__map_exclude.nii.gz:md5,44839611fb77fd588e99b9afa0ae6b91"
]
],
"pft_map_include": [
[
{
"id": "test"
},
"test__map_include.nii.gz:md5,f6ab6cb53316ab7d4672230e20aa0ea8"
"test__map_include.nii.gz:md5,d9983cec6fe4dbc7becce71ffac237b8"
]
],
"pft_seeding_mask": [
[
{
"id": "test"
},
"test__pft_seeding_mask.nii.gz:md5,1a824035733bd230eb82fd79c8ab6cdc"
"test__pft_seeding_mask.nii.gz:md5,3429293546e20469c84502394e37885d"
]
],
"pft_tractogram": [
[
{
"id": "test"
},
"test__pft_tracking.trk:md5,9234bb8361568b22baebd47d050fcedf"
"test__pft_tracking.trk:md5,38b3f540d2f112d5bbf026416b3d27ec"
]
],
"pulsation_in_b0": [
Expand All @@ -740,15 +740,15 @@
{
"id": "test"
},
"test__t1_warped.nii.gz:md5,8d02cdc310475e7d9f73ed7e61835f80"
"test__t1_warped.nii.gz:md5,e1d5080a5280df16a719c39825ce5ba2"
]
],
"t1_native": [
[
{
"id": "test"
},
"test_t1_cropped.nii.gz:md5,b31fd188e250502273f89c0c73c34628"
"test_t1_cropped.nii.gz:md5,c804e09ae12b053d76e10a3d74e98fb6"
]
],
"versions": [
Expand All @@ -774,15 +774,15 @@
{
"id": "test"
},
"test__map_wm.nii.gz:md5,c1fa90c2f2687dc206ee681a3420c525"
"test__map_wm.nii.gz:md5,cd10401b5feee8c2bc531b34612ac959"
]
],
"wm_mask": [
[
{
"id": "test"
},
"test__mask_wm.nii.gz:md5,82bf94c71fb31a2c73dd4ddc021b6d81"
"test__mask_wm.nii.gz:md5,d99f87e8fe4b713f85b8156bb00cb165"
]
],
"wmparc": [
Expand All @@ -794,6 +794,6 @@
"nf-test": "0.9.0",
"nextflow": "24.10.2"
},
"timestamp": "2024-12-17T19:37:33.475410485"
"timestamp": "2024-12-18T22:11:36.11074401"
}
}

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