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example_graph.dax
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example_graph.dax
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<?xml version="1.0" encoding="UTF-8"?>
<!-- generated: 2018-03-08 17:05:23.241822 -->
<!-- generated by: pipeline -->
<!-- generator: python -->
<adag xmlns="https://pegasus.isi.edu/schema/DAX" xmlns:xsi="https://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="https://pegasus.isi.edu/schema/DAX https://pegasus.isi.edu/schema/dax-3.6.xsd" version="3.6" name="TVB-PIPELINE">
<metadata key="created">Thu Mar 8 17:05:23 2018</metadata>
<job id="ID0000001" name="recon" node-label="Recon-all for T1">
<argument>TVB25 <file name="t1_input.nii.gz"/> 4 .a2009s</argument>
<uses name="t1_input.nii.gz" link="input"/>
<uses name="rh.aparc.a2009s.annot" link="output" register="true" transfer="true"/>
<uses name="lh.pial" link="output" register="true" transfer="true"/>
<uses name="brain.mgz" link="output" register="true" transfer="true"/>
<uses name="norm.mgz" link="output" register="true" transfer="true"/>
<uses name="aparc.a2009s+aseg.mgz" link="output" register="true" transfer="true"/>
<uses name="T1.mgz" link="output" register="true" transfer="true"/>
<uses name="lh.white" link="output" register="true" transfer="true"/>
<uses name="lh.aparc.a2009s.annot" link="output" register="true" transfer="true"/>
<uses name="rh.white" link="output" register="true" transfer="true"/>
<uses name="rh.pial" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000002" name="mri_convert" node-label="Convert T1 to NIFTI with good orientation">
<argument><file name="T1.mgz"/> <file name="T1.nii.gz"/> --out_orientation RAS</argument>
<uses name="T1.mgz" link="input"/>
<uses name="T1.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000003" name="mri_convert" node-label="Convert APARC+ASEG to NIFTI with good orientation">
<argument><file name="aparc.a2009s+aseg.mgz"/> <file name="aparc.a2009s+aseg.nii.gz"/> --out_orientation RAS -rt nearest</argument>
<uses name="aparc.a2009s+aseg.mgz" link="input"/>
<uses name="aparc.a2009s+aseg.nii.gz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000004" name="mrconvert">
<argument><file name="dwi_input_no_grad.nii"/> -fsl <file name="dwi.bvec"/> <file name="dwi.bval"/> <file name="dwi_input.mif"/></argument>
<uses name="dwi_input_no_grad.nii" link="input"/>
<uses name="dwi.bvec" link="input"/>
<uses name="dwi.bval" link="input"/>
<uses name="dwi_input.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000005" name="dwipreproc" node-label="DWI preprocessing">
<argument>ap <file name="dwi_input.mif"/> <file name="dwi.mif"/> -rpe_none -nthreads 2</argument>
<uses name="dwi_input.mif" link="input"/>
<uses name="dwi.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000006" name="dwi2mask" node-label="Create DWI mask">
<argument><file name="dwi.mif"/> <file name="mask.mif"/> -nthreads 2</argument>
<uses name="dwi.mif" link="input"/>
<uses name="mask.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000007" name="dwiextract" node-label="Extract DWI B0">
<argument><file name="dwi.mif"/> <file name="b0.nii.gz"/></argument>
<uses name="dwi.mif" link="input"/>
<uses name="b0.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000008" name="mrconvert">
<argument><file name="mask.mif"/> <file name="mask.nii.gz"/></argument>
<uses name="mask.mif" link="input"/>
<uses name="mask.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000009" name="qc_snapshot">
<argument>0 2vols <file name="mask.nii.gz"/> <file name="b0.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="mask.nii.gz" link="input"/>
<uses name="snapshot_axial_0.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_0.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_0.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000010" name="flirt" node-label="Register DWI to T1">
<argument><file name="b0.nii.gz"/> <file name="T1.nii.gz"/> <file name="d2t.mat"/> <file name="b0-in-t1.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="d2t.mat" link="output" register="true" transfer="true"/>
<uses name="b0-in-t1.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000011" name="qc_snapshot">
<argument>1 2vols <file name="T1.nii.gz"/> <file name="b0-in-t1.nii.gz"/></argument>
<uses name="b0-in-t1.nii.gz" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="snapshot_axial_1.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_1.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_1.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000012" name="convert-xfm" node-label="Convert d2t matrix to t2d matrix">
<argument>-omat <file name="t2d.mat"/> -inverse <file name="d2t.mat"/></argument>
<uses name="d2t.mat" link="input"/>
<uses name="t2d.mat" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000013" name="flirt-reversed" node-label="Register T1 to DWI">
<argument><file name="T1.nii.gz"/> <file name="b0.nii.gz"/> <file name="t1-in-d.nii.gz"/> <file name="t2d.mat"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="t2d.mat" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="t1-in-d.nii.gz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000014" name="qc_snapshot">
<argument>2 2vols <file name="t1-in-d.nii.gz"/> <file name="b0.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="snapshot_coronal_2.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_2.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_axial_2.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000015" name="flirt-reversed" node-label="Register APARC+ASEG to DWI">
<argument><file name="aparc.a2009s+aseg.nii.gz"/> <file name="b0.nii.gz"/> <file name="aparc.a2009s+aseg-in-d.nii.gz"/> <file name="t2d.mat"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="aparc.a2009s+aseg.nii.gz" link="input"/>
<uses name="t2d.mat" link="input"/>
<uses name="aparc.a2009s+aseg-in-d.nii.gz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000016" name="qc_snapshot">
<argument>3 2vols <file name="aparc.a2009s+aseg-in-d.nii.gz"/> <file name="b0.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="aparc.a2009s+aseg-in-d.nii.gz" link="input"/>
<uses name="snapshot_axial_3.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_3.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_3.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000017" name="qc_snapshot">
<argument>4 3vols <file name="t1-in-d.nii.gz"/> <file name="b0.nii.gz"/> <file name="aparc.a2009s+aseg-in-d.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="aparc.a2009s+aseg-in-d.nii.gz" link="input"/>
<uses name="snapshot_coronal_4.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_axial_4.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_4.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000018" name="aseg_concatenation">
<argument><file name="lh.aseg"/> <file name="lh.aseg.annot"/> "8 10 11 12 13 16 17 18 26" <file name="fs_color_lut.txt"/> TVB25</argument>
<uses name="aseg-000026" link="input"/>
<uses name="aseg-000010" link="input"/>
<uses name="fs_color_lut.txt" link="input"/>
<uses name="aseg-000013" link="input"/>
<uses name="aseg-000016" link="input"/>
<uses name="aseg-000012" link="input"/>
<uses name="aseg-000011" link="input"/>
<uses name="aseg-000018" link="input"/>
<uses name="aseg-000008" link="input"/>
<uses name="aseg-000017" link="input"/>
<uses name="lh.aseg" link="output" register="true" transfer="true"/>
<uses name="lh.aseg.annot" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000019" name="aseg_concatenation">
<argument><file name="rh.aseg"/> <file name="rh.aseg.annot"/> "47 49 50 51 52 53 54 58" <file name="fs_color_lut.txt"/> TVB25</argument>
<uses name="aseg-000058" link="input"/>
<uses name="fs_color_lut.txt" link="input"/>
<uses name="aseg-000050" link="input"/>
<uses name="aseg-000051" link="input"/>
<uses name="aseg-000049" link="input"/>
<uses name="aseg-000054" link="input"/>
<uses name="aseg-000053" link="input"/>
<uses name="aseg-000047" link="input"/>
<uses name="aseg-000052" link="input"/>
<uses name="rh.aseg" link="output" register="true" transfer="true"/>
<uses name="rh.aseg.annot" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000020" name="mri_pretess">
<argument><file name="aparc.a2009s+aseg.mgz"/> 8 <file name="norm.mgz"/> <file name="aseg-000008.mgz"/></argument>
<uses name="norm.mgz" link="input"/>
<uses name="aparc.a2009s+aseg.mgz" link="input"/>
<uses name="aseg-000008.mgz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000021" name="mri_tessellate">
<argument><file name="aseg-000008.mgz"/> 8 <file name="aseg-000008-notsmooth"/></argument>
<uses name="aseg-000008.mgz" link="input"/>
<uses name="aseg-000008-notsmooth" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000022" name="mris_extract_main_component">
<argument><file name="aseg-000008-notsmooth"/> <file name="lh.aseg-000008-notsmooth-main"/></argument>
<uses name="aseg-000008-notsmooth" link="input"/>
<uses name="lh.aseg-000008-notsmooth-main" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000023" name="mris_smooth">
<argument>-nw <file name="lh.aseg-000008-notsmooth-main"/> <file name="lh.aseg-000008"/></argument>
<uses name="lh.aseg-000008-notsmooth-main" link="input"/>
<uses name="lh.aseg-000008" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000024" name="mv">
<argument><file name="lh.aseg-000008"/> <file name="aseg-000008"/></argument>
<uses name="lh.aseg-000008" link="input"/>
<uses name="aseg-000008" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000025" name="mri_pretess">
<argument><file name="aparc.a2009s+aseg.mgz"/> 10 <file name="norm.mgz"/> <file name="aseg-000010.mgz"/></argument>
<uses name="norm.mgz" link="input"/>
<uses name="aparc.a2009s+aseg.mgz" link="input"/>
<uses name="aseg-000010.mgz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000026" name="mri_tessellate">
<argument><file name="aseg-000010.mgz"/> 10 <file name="aseg-000010-notsmooth"/></argument>
<uses name="aseg-000010.mgz" link="input"/>
<uses name="aseg-000010-notsmooth" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000027" name="mris_extract_main_component">
<argument><file name="aseg-000010-notsmooth"/> <file name="lh.aseg-000010-notsmooth-main"/></argument>
<uses name="aseg-000010-notsmooth" link="input"/>
<uses name="lh.aseg-000010-notsmooth-main" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000028" name="mris_smooth">
<argument>-nw <file name="lh.aseg-000010-notsmooth-main"/> <file name="lh.aseg-000010"/></argument>
<uses name="lh.aseg-000010-notsmooth-main" link="input"/>
<uses name="lh.aseg-000010" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000029" name="mv">
<argument><file name="lh.aseg-000010"/> <file name="aseg-000010"/></argument>
<uses name="lh.aseg-000010" link="input"/>
<uses name="aseg-000010" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000030" name="mri_pretess">
<argument><file name="aparc.a2009s+aseg.mgz"/> 11 <file name="norm.mgz"/> <file name="aseg-000011.mgz"/></argument>
<uses name="norm.mgz" link="input"/>
<uses name="aparc.a2009s+aseg.mgz" link="input"/>
<uses name="aseg-000011.mgz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000031" name="mri_tessellate">
<argument><file name="aseg-000011.mgz"/> 11 <file name="aseg-000011-notsmooth"/></argument>
<uses name="aseg-000011.mgz" link="input"/>
<uses name="aseg-000011-notsmooth" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000032" name="mris_extract_main_component">
<argument><file name="aseg-000011-notsmooth"/> <file name="lh.aseg-000011-notsmooth-main"/></argument>
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<uses name="lh.centered.aseg" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000106" name="mris_convert">
<argument>--to-scanner <file name="rh.aseg"/> <file name="rh.centered.aseg"/></argument>
<uses name="rh.aseg" link="input"/>
<uses name="rh.centered.aseg" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000107" name="mri_surf2surf">
<argument>.a2009s --srcsubject TVB25 --trgsubject fsaverage5 --hemi lh --sval-xyz pial --tval pial-fsaverage5 --tval-xyz <file name="T1.mgz"/></argument>
<uses name="T1.mgz" link="input"/>
<uses name="lh.pial" link="input"/>
<uses name="lh.pial-fsaverage5" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000108" name="mri_surf2surf">
<argument>.a2009s --srcsubject TVB25 --trgsubject fsaverage5 --hemi lh --sval-annot <file name="lh.aparc.a2009s.annot"/> --tval <file name="lh.aparc-fsaverage5.a2009s.annot"/></argument>
<uses name="lh.aparc.a2009s.annot" link="input"/>
<uses name="lh.aparc-fsaverage5.a2009s.annot" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000109" name="mri_surf2surf">
<argument>.a2009s --srcsubject TVB25 --trgsubject fsaverage5 --hemi rh --sval-xyz pial --tval pial-fsaverage5 --tval-xyz <file name="T1.mgz"/></argument>
<uses name="T1.mgz" link="input"/>
<uses name="rh.pial" link="input"/>
<uses name="rh.pial-fsaverage5" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000110" name="mri_surf2surf">
<argument>.a2009s --srcsubject TVB25 --trgsubject fsaverage5 --hemi rh --sval-annot <file name="rh.aparc.a2009s.annot"/> --tval <file name="rh.aparc-fsaverage5.a2009s.annot"/></argument>
<uses name="rh.aparc.a2009s.annot" link="input"/>
<uses name="rh.aparc-fsaverage5.a2009s.annot" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000111" name="mris_convert">
<argument>--to-scanner <file name="lh.pial-fsaverage5"/> <file name="lh.centered.pial-fsaverage5"/></argument>
<uses name="lh.pial-fsaverage5" link="input"/>
<uses name="lh.centered.pial-fsaverage5" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000112" name="mris_convert">
<argument>--to-scanner <file name="rh.pial-fsaverage5"/> <file name="rh.centered.pial-fsaverage5"/></argument>
<uses name="rh.pial-fsaverage5" link="input"/>
<uses name="rh.centered.pial-fsaverage5" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000113" name="qc_snapshot">
<argument>5 vol_surf <file name="T1.nii.gz"/> <file name="lh.centered.pial-fsaverage5"/> <file name="rh.centered.pial-fsaverage5"/></argument>
<uses name="T1.nii.gz" link="input"/>
<uses name="lh.centered.pial-fsaverage5" link="input"/>
<uses name="rh.centered.pial-fsaverage5" link="input"/>
<uses name="snapshot_sagittal_5.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_axial_5.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_5.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000114" name="qc_snapshot">
<argument>6 surf_annot <file name="lh.centered.pial-fsaverage5"/> <file name="lh.aparc-fsaverage5.a2009s.annot"/></argument>
<uses name="lh.aparc-fsaverage5.a2009s.annot" link="input"/>
<uses name="lh.centered.pial-fsaverage5" link="input"/>
<uses name="snapshot_surface_annotation_61.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_60.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_65.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_62.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_63.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_64.png" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000115" name="qc_snapshot">
<argument>7 surf_annot <file name="rh.centered.pial-fsaverage5"/> <file name="rh.aparc-fsaverage5.a2009s.annot"/></argument>
<uses name="rh.centered.pial-fsaverage5" link="input"/>
<uses name="rh.aparc-fsaverage5.a2009s.annot" link="input"/>
<uses name="snapshot_surface_annotation_70.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_73.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_72.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_75.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_71.png" link="output" register="true" transfer="true"/>
<uses name="snapshot_surface_annotation_74.png" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000116" name="gen_mapping_details">
<argument>.a2009s <file name="fs_color_lut.txt"/> <file name="T1.nii.gz"/> <file name="lh.centered.pial-fsaverage5"/> <file name="rh.centered.pial-fsaverage5"/> <file name="lh.aparc-fsaverage5.a2009s.annot"/> <file name="rh.aparc-fsaverage5.a2009s.annot"/> <file name="lh.centered.aseg"/> <file name="rh.centered.aseg"/> <file name="lh.aseg.annot"/> <file name="rh.aseg.annot"/></argument>
<uses name="rh.centered.aseg" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="lh.aparc-fsaverage5.a2009s.annot" link="input"/>
<uses name="rh.centered.pial-fsaverage5" link="input"/>
<uses name="rh.aparc-fsaverage5.a2009s.annot" link="input"/>
<uses name="fs_color_lut.txt" link="input"/>
<uses name="rh.aseg.annot" link="input"/>
<uses name="lh.aseg.annot" link="input"/>
<uses name="lh.centered.pial-fsaverage5" link="input"/>
<uses name="lh.centered.aseg" link="input"/>
<uses name="centers.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="rm_to_aparc_aseg.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="cortical.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="rh_dipoles.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="areas.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="region_mapping_cort.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="surface_cort.zip" link="output" register="true" transfer="true"/>
<uses name="lh_dipoles.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="region_mapping_subcort.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="average_orientations.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="fs_custom.a2009s.txt" link="output" register="true" transfer="true"/>
<uses name="surface_subcort.zip" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000117" name="ttgen" node-label="Generate 5tt MIF">
<argument><file name="t1-in-d.nii.gz"/> <file name="5tt.mif"/></argument>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="5tt.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000118" name="tt2gmwmi" node-label="Extract GMWMI">
<argument><file name="5tt.mif"/> <file name="gmwmi.mif"/> -nthreads 2</argument>
<uses name="5tt.mif" link="input"/>
<uses name="gmwmi.mif" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000119" name="mrconvert">
<argument><file name="gmwmi.mif"/> <file name="gmwmi.nii.gz"/></argument>
<uses name="gmwmi.mif" link="input"/>
<uses name="gmwmi.nii.gz" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000120" name="qc_snapshot">
<argument>8 2vols <file name="t1-in-d.nii.gz"/> <file name="gmwmi.nii.gz"/></argument>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="gmwmi.nii.gz" link="input"/>
<uses name="snapshot_axial_8.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_8.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_8.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000121" name="tt2vis" node-label="Generate TT2VIS MIF">
<argument><file name="5tt.mif"/> <file name="5ttvis.mif"/></argument>
<uses name="5tt.mif" link="input"/>
<uses name="5ttvis.mif" link="output" register="false" transfer="false"/>
</job>
<job id="ID0000122" name="dwi2response" node-label="Compute the DWI Response">
<argument><file name="dwi.mif"/> <file name="response.txt"/> <file name="mask.mif"/></argument>
<uses name="mask.mif" link="input"/>
<uses name="dwi.mif" link="input"/>
<uses name="response.txt" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000123" name="dwi2fod" node-label="Obtain WM FOD">
<argument>csd <file name="dwi.mif"/> <file name="response.txt"/> <file name="wm_fod.mif"/> -mask <file name="mask.mif"/> -nthreads 2</argument>
<uses name="mask.mif" link="input"/>
<uses name="response.txt" link="input"/>
<uses name="dwi.mif" link="input"/>
<uses name="wm_fod.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000124" name="tckgen" node-label="Generate tracts">
<argument><file name="wm_fod.mif"/> <file name="5M.tck"/> -number 5M -seed_gmwmi <file name="gmwmi.mif"/> -act <file name="5tt.mif"/> -unidirectional -maxlength 250 -step 0.5 -nthreads 2</argument>
<uses name="wm_fod.mif" link="input"/>
<uses name="5tt.mif" link="input"/>
<uses name="gmwmi.mif" link="input"/>
<uses name="5M.tck" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000125" name="tcksift" node-label="Tracts SIFT">
<argument><file name="5M.tck"/> <file name="wm_fod.mif"/> <file name="2M.tck"/> -term_number 2M -act <file name="5tt.mif"/> -nthreads 2</argument>
<uses name="wm_fod.mif" link="input"/>
<uses name="5M.tck" link="input"/>
<uses name="5tt.mif" link="input"/>
<uses name="2M.tck" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000126" name="tckmap" node-label="TCKMAP">
<argument><file name="2M.tck"/> <file name="tdi_ends.mif"/> -vox 1 -template <file name="b0.nii.gz"/></argument>
<uses name="b0.nii.gz" link="input"/>
<uses name="2M.tck" link="input"/>
<uses name="tdi_ends.mif" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000127" name="mrconvert">
<argument><file name="tdi_ends.mif"/> <file name="tdi_ends.nii.gz"/></argument>
<uses name="tdi_ends.mif" link="input"/>
<uses name="tdi_ends.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000128" name="qc_snapshot">
<argument>9 2vols <file name="t1-in-d.nii.gz"/> <file name="tdi_ends.nii.gz"/></argument>
<uses name="tdi_ends.nii.gz" link="input"/>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="snapshot_axial_9.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_9.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_sagittal_9.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000129" name="labelconvert" node-label="Compute APARC+ASEG labeled for tracts">
<argument><file name="aparc.a2009s+aseg-in-d.nii.gz"/> <file name="fs_color_lut.txt"/> <file name="fs_custom.a2009s.txt"/> <file name="volume_lbl.a2009s.nii.gz"/></argument>
<uses name="fs_custom.a2009s.txt" link="input"/>
<uses name="aparc.a2009s+aseg-in-d.nii.gz" link="input"/>
<uses name="fs_color_lut.txt" link="input"/>
<uses name="volume_lbl.a2009s.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000130" name="qc_snapshot">
<argument>10 2vols <file name="t1-in-d.nii.gz"/> <file name="volume_lbl.a2009s.nii.gz"/></argument>
<uses name="volume_lbl.a2009s.nii.gz" link="input"/>
<uses name="t1-in-d.nii.gz" link="input"/>
<uses name="snapshot_sagittal_10.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_coronal_10.png" link="output" register="false" transfer="true"/>
<uses name="snapshot_axial_10.png" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000131" name="tck2connectome" node-label="Generate weigths">
<argument><file name="2M.tck"/> <file name="volume_lbl.a2009s.nii.gz"/> -assignment_radial_search 2 <file name="tract_counts.a2009s.csv"/></argument>
<uses name="volume_lbl.a2009s.nii.gz" link="input"/>
<uses name="2M.tck" link="input"/>
<uses name="tract_counts.a2009s.csv" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000132" name="tck2connectome" node-label="Generate tract lengths">
<argument><file name="2M.tck"/> <file name="volume_lbl.a2009s.nii.gz"/> -assignment_radial_search 2 -scale_length -stat_edge mean <file name="tract_lengths.a2009s.csv"/></argument>
<uses name="volume_lbl.a2009s.nii.gz" link="input"/>
<uses name="2M.tck" link="input"/>
<uses name="tract_lengths.a2009s.csv" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000133" name="convert_output">
<argument><file name="tract_counts.a2009s.csv"/> <file name="tract_lengths.a2009s.csv"/> .a2009s</argument>
<uses name="centers.a2009s.txt" link="input"/>
<uses name="rm_to_aparc_aseg.a2009s.txt" link="input"/>
<uses name="cortical.a2009s.txt" link="input"/>
<uses name="tract_counts.a2009s.csv" link="input"/>
<uses name="average_orientations.a2009s.txt" link="input"/>
<uses name="areas.a2009s.txt" link="input"/>
<uses name="aparc.a2009s+aseg.nii.gz" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="tract_lengths.a2009s.csv" link="input"/>
<uses name="aparc+aseg-cor.a2009s.nii.gz" link="output" register="false" transfer="true"/>
<uses name="connectivity.a2009s.zip" link="output" register="false" transfer="true"/>
</job>
<job id="ID0000134" name="mne_watershed_bem">
<argument>TVB25</argument>
<uses name="TVB25_inner_skull_surface" link="output" register="true" transfer="true"/>
<uses name="TVB25_outer_skin_surface" link="output" register="true" transfer="true"/>
<uses name="TVB25_brain_surface" link="output" register="true" transfer="true"/>
<uses name="TVB25_outer_skull_surface" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000135" name="mris_convert">
<argument>--to-scanner <file name="TVB25_brain_surface"/> <file name="rh.centered.TVB25_brain_surface"/></argument>
<uses name="TVB25_brain_surface" link="input"/>
<uses name="rh.centered.TVB25_brain_surface" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000136" name="mris_convert">
<argument>--to-scanner <file name="TVB25_inner_skull_surface"/> <file name="rh.centered.TVB25_inner_skull_surface"/></argument>
<uses name="TVB25_inner_skull_surface" link="input"/>
<uses name="rh.centered.TVB25_inner_skull_surface" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000137" name="mris_convert">
<argument>--to-scanner <file name="TVB25_outer_skin_surface"/> <file name="rh.centered.TVB25_outer_skin_surface"/></argument>
<uses name="TVB25_outer_skin_surface" link="input"/>
<uses name="rh.centered.TVB25_outer_skin_surface" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000138" name="mris_convert">
<argument>--to-scanner <file name="TVB25_outer_skull_surface"/> <file name="rh.centered.TVB25_outer_skull_surface"/></argument>
<uses name="TVB25_outer_skull_surface" link="input"/>
<uses name="rh.centered.TVB25_outer_skull_surface" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000139" name="generate_surface_zip">
<argument><file name="rh.centered.TVB25_brain_surface"/> <file name="TVB25_brain_surface.zip"/> TVB25</argument>
<uses name="rh.centered.TVB25_brain_surface" link="input"/>
<uses name="TVB25_brain_surface.zip" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000140" name="generate_surface_zip">
<argument><file name="rh.centered.TVB25_inner_skull_surface"/> <file name="TVB25_inner_skull_surface.zip"/> TVB25</argument>
<uses name="rh.centered.TVB25_inner_skull_surface" link="input"/>
<uses name="TVB25_inner_skull_surface.zip" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000141" name="generate_surface_zip">
<argument><file name="rh.centered.TVB25_outer_skin_surface"/> <file name="TVB25_outer_skin_surface.zip"/> TVB25</argument>
<uses name="rh.centered.TVB25_outer_skin_surface" link="input"/>
<uses name="TVB25_outer_skin_surface.zip" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000142" name="generate_surface_zip">
<argument><file name="rh.centered.TVB25_outer_skull_surface"/> <file name="TVB25_outer_skull_surface.zip"/> TVB25</argument>
<uses name="rh.centered.TVB25_outer_skull_surface" link="input"/>
<uses name="TVB25_outer_skull_surface.zip" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000143" name="mri_convert">
<argument><file name="ct_input.nii.gz"/> <file name="ct-ras.nii.gz"/> --out_orientation RAS</argument>
<uses name="ct_input.nii.gz" link="input"/>
<uses name="ct-ras.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000144" name="flirt">
<argument><file name="ct-ras.nii.gz"/> <file name="T1.nii.gz"/> <file name="ct_to_t1.mat"/> <file name="ct-in-t1.nii.gz"/></argument>
<uses name="ct-ras.nii.gz" link="input"/>
<uses name="T1.nii.gz" link="input"/>
<uses name="ct_to_t1.mat" link="output" register="true" transfer="true"/>
<uses name="ct-in-t1.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000145" name="mri_convert">
<argument><file name="brain.mgz"/> <file name="brain-ras.nii.gz"/> --out_orientation RAS</argument>
<uses name="brain.mgz" link="input"/>
<uses name="brain-ras.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000146" name="mri_binarize">
<argument>--i <file name="brain-ras.nii.gz"/> --o <file name="brain-mask.nii.gz"/> --min 10 --erode 4</argument>
<uses name="brain-ras.nii.gz" link="input"/>
<uses name="brain-mask.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000147" name="mri_binarize">
<argument>--i <file name="ct-in-t1.nii.gz"/> --o <file name="masked-ct.nii.gz"/> --min 1000 --mask <file name="brain-mask.nii.gz"/></argument>
<uses name="ct-in-t1.nii.gz" link="input"/>
<uses name="brain-mask.nii.gz" link="input"/>
<uses name="masked-ct.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000148" name="mri_binarize">
<argument>--i <file name="masked-ct.nii.gz"/> --o <file name="dilated-ct.nii.gz"/> --min 0.5 --dilate 2 --erode 1</argument>
<uses name="masked-ct.nii.gz" link="input"/>
<uses name="dilated-ct.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000149" name="label_ct_with_dilation">
<argument><file name="masked-ct.nii.gz"/> <file name="dilated-ct.nii.gz"/> <file name="labeled-ct.nii.gz"/> TVB25</argument>
<uses name="masked-ct.nii.gz" link="input"/>
<uses name="dilated-ct.nii.gz" link="input"/>
<uses name="labeled-ct.nii.gz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000150" name="gen_schema_txt">
<argument><file name="labeled-ct.nii.gz"/> <file name="schema.txt"/></argument>
<uses name="labeled-ct.nii.gz" link="input"/>
<uses name="schema.txt" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000151" name="gen_seeg_xyz">
<argument><file name="labeled-ct.nii.gz"/> <file name="schema.txt"/> <file name="seeg.xyz"/> TVB25</argument>
<uses name="labeled-ct.nii.gz" link="input"/>
<uses name="schema.txt" link="input"/>
<uses name="seeg.xyz" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000152" name="compute_projection_matrix">
<argument><file name="seeg.xyz"/> <file name="centers.a2009s.txt"/> <file name="seeg_dp_gain.a2009s.mat"/> TVB25</argument>
<uses name="seeg.xyz" link="input"/>
<uses name="centers.a2009s.txt" link="input"/>
<uses name="seeg_dp_gain.a2009s.mat" link="output" register="true" transfer="true"/>
</job>
<job id="ID0000153" name="compute_seeg_gain">
<argument><file name="seeg.xyz"/> <file name="surface_cort.zip"/> <file name="surface_subcort.zip"/> <file name="region_mapping_cort.a2009s.txt"/> <file name="region_mapping_subcort.a2009s.txt"/> <file name="seeg_mrs_gain.a2009s.mat"/> TVB25</argument>
<uses name="surface_cort.zip" link="input"/>
<uses name="region_mapping_cort.a2009s.txt" link="input"/>
<uses name="region_mapping_subcort.a2009s.txt" link="input"/>
<uses name="surface_subcort.zip" link="input"/>
<uses name="seeg.xyz" link="input"/>
<uses name="seeg_mrs_gain.a2009s.mat" link="output" register="true" transfer="true"/>
</job>
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<parent ref="ID0000001"/>
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<child ref="ID0000006">
<parent ref="ID0000005"/>
</child>
<child ref="ID0000007">
<parent ref="ID0000005"/>
</child>
<child ref="ID0000008">
<parent ref="ID0000006"/>
</child>
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<parent ref="ID0000008"/>
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<parent ref="ID0000007"/>
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<child ref="ID0000011">
<parent ref="ID0000010"/>
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<child ref="ID0000012">
<parent ref="ID0000010"/>
</child>
<child ref="ID0000013">
<parent ref="ID0000012"/>
</child>
<child ref="ID0000014">
<parent ref="ID0000013"/>
</child>
<child ref="ID0000015">
<parent ref="ID0000003"/>
<parent ref="ID0000012"/>
</child>
<child ref="ID0000016">
<parent ref="ID0000015"/>
</child>
<child ref="ID0000017">
<parent ref="ID0000013"/>
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