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@@ -60,7 +60,8 @@ participantField='ParticipantId'
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ds=db.selectRows(project,'study',dataset,[])
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#imageSelector={"CT":"CT","PET":"PETWB"};
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imageSelector={"CT":"CT_orthancId","PET":"PETWB_orthancId"}
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-imageResampledField={"CT":"ctResampled","PET":"petResampled"}
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+#output
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+imageResampledField={"CT":"ctResampled","PET":"petResampled","patientmask":"ROImask"}
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#projectNIfTIBase=os.path.join(labkeyBase,'files',project,'@files/nifti')
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#use webdav to transfer file (even though it is localhost)
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@@ -154,7 +155,7 @@ for row in ds["rows"]:
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volumeFileNames={im:\
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getStudyLabel(row,participantField)+'_'+im+
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'_notCropped_2mmVoxel.nii'\
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- for im in imageSelector}
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+ for im in imageResampledField}
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gzFileNames={im:f+".gz" \
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for (im,f) in volumeFileNames.items()}
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@@ -207,6 +208,7 @@ for row in ds["rows"]:
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if not all(filesPresent):
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+ #use imageSelector -> inputs
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for im in imageSelector:
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#checks if raw files are already loaded
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getDicom(ofb,row,zipDir,rawDir,im,imageSelector,\
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