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...ydneyimaging/australianimagingservice/community/au/edu/sydney/sydneyimaging/t1_preproc.py
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,138 +1,138 @@ | ||
| from pydra import Workflow | ||
| from pydra.engine.specs import File | ||
| from pydra.tasks.mrtrix3.v3_0 import ( | ||
| fivett2vis, | ||
| fivettgen_hsvs, | ||
| labelconvert, | ||
| labelsgmfix, | ||
| ) | ||
| # from pydra.tasks.mrtrix3.v3_0 import ( | ||
| # fivett2vis, | ||
| # fivettgen_hsvs, | ||
| # labelconvert, | ||
| # labelsgmfix, | ||
| # ) | ||
| from fileformats.medimage import NiftiGz, MghGz | ||
| from fileformats.medimage_mrtrix3 import ImageFormat as MIF | ||
| from pydra.tasks.fastsurfer.latest import fastsurfer | ||
| # from pydra.tasks.fastsurfer.latest import fastsurfer | ||
|
|
||
|
|
||
| def t1_preproc(): | ||
| # Define the path and output_path variables | ||
| # path = '/Users/arkievdsouza/Documents/NIFdata/ds000114' | ||
| output_path = "/Users/arkievdsouza/git/t1-pipeline/working-dir" | ||
|
|
||
| # Define the input_spec for the workflow | ||
| input_spec = { | ||
| "t1w": NiftiGz, | ||
| "fs_license": File, | ||
| "sub_ID": str, | ||
| "default_file": File, | ||
| "freesurfer_LUT": File, | ||
| "segmentation": MghGz, | ||
| } | ||
| output_spec = {"fTT_image": MIF, "vis_image": MIF, "parc_image": MIF} | ||
|
|
||
| # Create a workflow | ||
| wf = Workflow( | ||
| name="T1preproc_workflow", | ||
| input_spec=input_spec, | ||
| cache_dir=output_path, | ||
| output_spec=output_spec, | ||
| ) | ||
|
|
||
| # FastSurfer Task | ||
| wf.add( | ||
| fastsurfer( | ||
| T1_files=wf.lzin.t1w, | ||
| fs_license=wf.lzin.fs_license, | ||
| subject_id=wf.lzin.sub_ID, | ||
| threads=7, | ||
| parallel=True, | ||
| name="FastSurfer_task", | ||
| py="python3.11", | ||
| norm_img="norm.nii.gz", | ||
| aparcaseg="aparcaseg.nii.gz", | ||
| surf_only=True, | ||
| seg=wf.lzin.segmentation, | ||
| ) | ||
| ) | ||
|
|
||
| # ################################################# | ||
| # # Five Tissue Type Generation and visualisation # | ||
| # ################################################# | ||
|
|
||
| # Five tissue-type task | ||
| wf.add( | ||
| fivettgen_hsvs( | ||
| input=wf.FastSurfer_task.lzout.subjects_dir, | ||
| output="fTT_hsvs.mif", | ||
| name="fTTgen_task", | ||
| nocrop=True, | ||
| nocleanup=True, | ||
| white_stem=True, | ||
| ) | ||
| ) | ||
|
|
||
| # Five tissue-type visualisation task | ||
| wf.add( | ||
| fivett2vis( | ||
| input=wf.fTTgen_task.lzout.output.cast(MIF), | ||
| output="fTT_hsvs_vis.mif", | ||
| name="fTTvis_task", | ||
| ) | ||
| ) | ||
|
|
||
| # ################### | ||
| # # DK parcellation # | ||
| # ################### | ||
|
|
||
| # relabel segmenetation to integers indexed from 1 to 84 | ||
| wf.add( | ||
| labelconvert( | ||
| path_in=wf.FastSurfer_task.lzout.aparcaseg_img, | ||
| lut_in=wf.lzin.freesurfer_LUT, | ||
| lut_out=wf.lzin.default_file, | ||
| path_out="nodes.mif", | ||
| name="LabelConvert_task", | ||
| ) | ||
| ) | ||
|
|
||
| # # Replace FreeSurfer’s estimates of sub-cortical grey matter structures with estimates from FSL’s FIRST tool | ||
| wf.add( | ||
| labelsgmfix( | ||
| parc=wf.LabelConvert_task.lzout.path_out, | ||
| t1=wf.FastSurfer_task.lzout.norm_img, | ||
| lut=wf.lzin.default_file, | ||
| output="parcellation_image_DK_unregistered.mif", | ||
| name="SGMfix_task", | ||
| nocleanup=True, | ||
| premasked=True, | ||
| sgm_amyg_hipp=True, | ||
| ) | ||
| ) | ||
|
|
||
| ################## | ||
| # WORKFLOW SETUP # | ||
| ################## | ||
|
|
||
| wf.set_output(("fTT_image", wf.fTTgen_task.lzout.output.cast(MIF))) | ||
| wf.set_output(("vis_image", wf.fTTvis_task.lzout.output.cast(MIF))) | ||
| wf.set_output(("parc_image", wf.SGMfix_task.lzout.output.cast(MIF))) | ||
|
|
||
| # ## Execute the workflow (FastSurfer, NIF data) | ||
| # # Define the input_spec for the workflow | ||
| # input_spec = { | ||
| # "t1w": NiftiGz, | ||
| # "fs_license": File, | ||
| # "sub_ID": str, | ||
| # "default_file": File, | ||
| # "freesurfer_LUT": File, | ||
| # "segmentation": MghGz, | ||
| # } | ||
| # output_spec = {"fTT_image": MIF, "vis_image": MIF, "parc_image": MIF} | ||
|
|
||
| # # Create a workflow | ||
| # wf = Workflow( | ||
| # name="T1preproc_workflow", | ||
| # input_spec=input_spec, | ||
| # cache_dir=output_path, | ||
| # output_spec=output_spec, | ||
| # ) | ||
|
|
||
| # # FastSurfer Task | ||
| # wf.add( | ||
| # fastsurfer( | ||
| # T1_files=wf.lzin.t1w, | ||
| # fs_license=wf.lzin.fs_license, | ||
| # subject_id=wf.lzin.sub_ID, | ||
| # threads=7, | ||
| # parallel=True, | ||
| # name="FastSurfer_task", | ||
| # py="python3.11", | ||
| # norm_img="norm.nii.gz", | ||
| # aparcaseg="aparcaseg.nii.gz", | ||
| # surf_only=True, | ||
| # seg=wf.lzin.segmentation, | ||
| # ) | ||
| # ) | ||
|
|
||
| # # ################################################# | ||
| # # # Five Tissue Type Generation and visualisation # | ||
| # # ################################################# | ||
|
|
||
| # # Five tissue-type task | ||
| # wf.add( | ||
| # fivettgen_hsvs( | ||
| # input=wf.FastSurfer_task.lzout.subjects_dir, | ||
| # output="fTT_hsvs.mif", | ||
| # name="fTTgen_task", | ||
| # nocrop=True, | ||
| # nocleanup=True, | ||
| # white_stem=True, | ||
| # ) | ||
| # ) | ||
|
|
||
| # # Five tissue-type visualisation task | ||
| # wf.add( | ||
| # fivett2vis( | ||
| # input=wf.fTTgen_task.lzout.output.cast(MIF), | ||
| # output="fTT_hsvs_vis.mif", | ||
| # name="fTTvis_task", | ||
| # ) | ||
| # ) | ||
|
|
||
| # # ################### | ||
| # # # DK parcellation # | ||
| # # ################### | ||
|
|
||
| # # relabel segmenetation to integers indexed from 1 to 84 | ||
| # wf.add( | ||
| # labelconvert( | ||
| # path_in=wf.FastSurfer_task.lzout.aparcaseg_img, | ||
| # lut_in=wf.lzin.freesurfer_LUT, | ||
| # lut_out=wf.lzin.default_file, | ||
| # path_out="nodes.mif", | ||
| # name="LabelConvert_task", | ||
| # ) | ||
| # ) | ||
|
|
||
| # # # Replace FreeSurfer’s estimates of sub-cortical grey matter structures with estimates from FSL’s FIRST tool | ||
| # wf.add( | ||
| # labelsgmfix( | ||
| # parc=wf.LabelConvert_task.lzout.path_out, | ||
| # t1=wf.FastSurfer_task.lzout.norm_img, | ||
| # lut=wf.lzin.default_file, | ||
| # output="parcellation_image_DK_unregistered.mif", | ||
| # name="SGMfix_task", | ||
| # nocleanup=True, | ||
| # premasked=True, | ||
| # sgm_amyg_hipp=True, | ||
| # ) | ||
| # ) | ||
|
|
||
| # ################## | ||
| # # WORKFLOW SETUP # | ||
| # ################## | ||
|
|
||
| # wf.set_output(("fTT_image", wf.fTTgen_task.lzout.output.cast(MIF))) | ||
| # wf.set_output(("vis_image", wf.fTTvis_task.lzout.output.cast(MIF))) | ||
| # wf.set_output(("parc_image", wf.SGMfix_task.lzout.output.cast(MIF))) | ||
|
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||
| # # ## Execute the workflow (FastSurfer, NIF data) | ||
| # # result = wf( | ||
| # # t1w="/Users/arkievdsouza/Documents/NIFdata/ds000114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz", | ||
| # # fs_license="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FS_license.txt", | ||
| # # sub_ID="sub-01_ses-retest", | ||
| # # plugin="serial" | ||
| # # ) | ||
|
|
||
| # # Execute the workflow (FastSurfer, HCP data) | ||
| # result = wf( | ||
| # t1w="/Users/arkievdsouza/Documents/NIFdata/ds000114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz", | ||
| # t1w="/Users/arkievdsouza/Documents/100307/100307_FastSurfer/mri/orig.nii.gz", | ||
| # fs_license="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FS_license.txt", | ||
| # sub_ID="sub-01_ses-retest", | ||
| # plugin="serial" | ||
| # sub_ID="100307", | ||
| # default_file="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/fs_default.txt", | ||
| # freesurfer_LUT="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FreeSurferColorLUT.txt", | ||
| # segmentation="/Users/arkievdsouza/git/t1-pipeline/working-dir/fastsurfer_0425d50a2d1bdc642ef8feb235ec3855/subjects_dir/100307/mri/aparc.DKTatlas+aseg.deep.mgz", | ||
| # plugin="serial", | ||
| # ) | ||
|
|
||
| # Execute the workflow (FastSurfer, HCP data) | ||
| result = wf( | ||
| t1w="/Users/arkievdsouza/Documents/100307/100307_FastSurfer/mri/orig.nii.gz", | ||
| fs_license="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FS_license.txt", | ||
| sub_ID="100307", | ||
| default_file="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/fs_default.txt", | ||
| freesurfer_LUT="/Users/arkievdsouza/Desktop/FastSurferTesting/ReferenceFiles/FreeSurferColorLUT.txt", | ||
| segmentation="/Users/arkievdsouza/git/t1-pipeline/working-dir/fastsurfer_0425d50a2d1bdc642ef8feb235ec3855/subjects_dir/100307/mri/aparc.DKTatlas+aseg.deep.mgz", | ||
| plugin="serial", | ||
| ) | ||
|
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||
| # print(f"Processed output generated at '{result.output.dwi_preproc}'") | ||
|
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||
| # create_dotfile |