diff --git a/Dockerfile_testpypi b/Dockerfile_testpypi index 019e82b..f5d0a6e 100644 --- a/Dockerfile_testpypi +++ b/Dockerfile_testpypi @@ -46,8 +46,9 @@ RUN pip3 install xvfbwrapper \ pbr \ nibabel==3.2.2 \ packaging \ - pytest \ - install \ + pytest + +RUN pip3 install install \ graphviz \ pybids \ nipype \ diff --git a/skullTo3d/_version.py b/skullTo3d/_version.py index 4a48739..ffcc925 100644 --- a/skullTo3d/_version.py +++ b/skullTo3d/_version.py @@ -1,2 +1 @@ - __version__ = '0.0.3' diff --git a/skullTo3d/pipelines/skull_pipe.py b/skullTo3d/pipelines/skull_pipe.py index e046bc1..3f66efb 100644 --- a/skullTo3d/pipelines/skull_pipe.py +++ b/skullTo3d/pipelines/skull_pipe.py @@ -374,6 +374,8 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}): align_ct_on_T1 = pe.Node(interface=RegAladin(), name="align_ct_on_T1") + align_ct_on_T1.inputs.rig_only_flag = True + skull_ct_pipe.connect(inputnode, 'ct', align_ct_on_T1, "flo_file") @@ -411,7 +413,7 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}): inputnode, ("indiv_params", parse_key, "ct_skull_mask_thr"), ct_skull_mask_thr, "indiv_params") - skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file", + skull_ct_pipe.connect(align_ct_on_stereo_T1, 'out_file', ct_skull_mask_thr, "in_file") else: @@ -426,7 +428,7 @@ def create_skull_ct_pipe(name="skull_ct_pipe", params={}): params=parse_key(params, "ct_skull_auto_mask"), name="ct_skull_auto_mask") - skull_ct_pipe.connect(align_ct_on_stereo_T1, "out_file", + skull_ct_pipe.connect(align_ct_on_stereo_T1, 'out_file', ct_skull_auto_mask, "img_file") skull_ct_pipe.connect( @@ -849,7 +851,6 @@ def create_skull_petra_pipe(name="skull_petra_pipe", params={}): if "petra_skull_fov" in params.keys(): # petra_skull_fov ####### [okey][json] - petra_skull_fov = NodeParams( interface=RobustFOV(), params=parse_key(params, "petra_skull_fov"), diff --git a/workflows/params_segment_macaque_ants_skull.json b/workflows/params_segment_macaque_ants_skull.json index 44d3353..5b0a7d1 100755 --- a/workflows/params_segment_macaque_ants_skull.json +++ b/workflows/params_segment_macaque_ants_skull.json @@ -157,7 +157,7 @@ "t1_head_erode_skin": { "kernel_shape": "boxv", - "kernel_size": 18.0 + "kernel_size": 9.0 }, "t1_skull_dilate": { @@ -179,11 +179,11 @@ { "ct_skull_auto_mask": { - "kmeans": false, + "kmeans": true, "sample_bins": 30, "distance": 10, - "operation": "higher", - "index": 3 + "operation": "lower", + "index": 2 }, "ct_skull_dilate": { diff --git a/workflows/segment_petra.py b/workflows/segment_petra.py index 8896f42..e845d81 100644 --- a/workflows/segment_petra.py +++ b/workflows/segment_petra.py @@ -839,7 +839,7 @@ def create_main_workflow(data_dir, process_dir, soft, species, subjects, datasink, '@t1_native_skull_mask') if "ct" in skull_dt and "skull_ct_pipe" in params.keys(): - print("rename ct skull pipe") + print("rename ct skull pipe 1") rename_all_skull_ct_derivatives( params, main_workflow, segment_brain_pipe, skull_ct_pipe,