CTSC DataManagementWorkflow - Revision history

Mark at 23:30, 10 November 2009

2009-11-10T23:30:07Z

2009-11-10T23:03:54Z

2009-11-10T21:02:05Z

2009-11-10T20:39:09Z

2009-11-10T20:32:21Z

2009-11-10T20:31:49Z

2009-11-10T20:19:28Z

2009-11-10T20:16:06Z

2009-11-10T20:12:21Z

2009-11-10T20:03:25Z

@@ Line 68: / Line 68: @@
    (0020,0011) := "10"
-and 2) create new a new SOPInstanceUID for each image in the derived series with the following script that uses the dcmtk tool dcmodify:
+) create new a new SOPInstanceUID for each image in the derived series with the following script that uses the dcmtk tool dcmodify:
   #!/bin/tcsh
@@ Line 86: / Line 86: @@
   @ i++
   end
 * Case3 - FMRI data upload - Below is the essense of an email that I sent to the xnat discussion group that I never

@@ Line 62: / Line 62: @@
 [[File:seg.png]] [ Labelled colon segmentation on xnat central]
-Obviously,we will need a more elegant solution to upload data derived in this fashion in the future.
+To solve this derived data case, 1) apply a separate .das file that contains new series description
 * Case3 - FMRI data upload - Below is the essense of an email that I sent to the xnat discussion group that I never
 heard back from:

@@ Line 47: / Line 47: @@
 anonymizing is performed during this step as well.
-* Case 2 - Upload of segmentations derived from DICOM data. This is even more problematic, depending on the situation. I am currently
+* Case 2 - Upload of segmentations derived from DICOM data. This can be  even more problematic, depending on the situation. I am currently
 uploading prostate segmentations combined with the original DICOM data. Each subject has several MRI series and an expert labelmap
 segmentation that need to be uploaded as a single subject. The researcher's approach was to create a new series number for the segmentation,
@@ Line 60: / Line 60: @@
 Here is the segmented data in xnat:
-[[File:seg.png]] [ Labelled colon segmentation]
+[[File:seg.png]] [ Labelled colon segmentation on xnat central]
 Obviously,we will need a more elegant solution to upload data derived in this fashion in the future.

@@ Line 70: / Line 70: @@
 the fmri task being performed for each series via the .das file.
 During the upload process, I get a  proxy error:
 [[File:xnat-proxy-error.jpg]]
- But sometime later my data shows
 up in the prearchive and appears  complete and intact and I can move it to the project. However, when
 I then select the subject from the project,  I see a processing exception at the top of the page:
 [[File:process-error.jpg]]
 I am concerned that when we go to share the data after uploading everything, if someone sees this processing
 exception they will figure the data is corrupt whereas it is complete and wont use it. So I am curious:

@@ Line 70: / Line 70: @@
 the fmri task being performed for each series via the .das file.
 During the upload process, I get a  proxy error:
-[[File:proxy-error.jpg]]
+[[File:xnat-proxy-error.jpg]]
   But sometime later my data shows
 up in the prearchive and appears  complete and intact and I can move it to the project. However, when

@@ Line 63: / Line 63: @@
 Obviously,we will need a more elegant solution to upload data derived in this fashion in the future.
 ==Target Data Management Process Option B. batch scripted upload via DICOM Server (Yong Gao) '''CURRENTLY BEING DEVELOPED'''==
 * Create new project using web GUI

← Older revision		Revision as of 20:19, 10 November 2009
Line 61:		Line 61:

	[[File:seg.png]] [ Labelled colon segmentation]		[[File:seg.png]] [ Labelled colon segmentation]
		+
		+	Obviously,we will need a more elegant solution to upload data derived in this fashion in the future.
		+

	==Target Data Management Process Option B. batch scripted upload via DICOM Server (Yong Gao) '''CURRENTLY BEING DEVELOPED'''==		==Target Data Management Process Option B. batch scripted upload via DICOM Server (Yong Gao) '''CURRENTLY BEING DEVELOPED'''==

@@ Line 59: / Line 59: @@
   (0020,000e) := "1.2.840.113619.2.207.3596.11861984.25740.1219404288.477"
 Here is the segmented data in xnat:
-[[Image:seg.png|frame| Labelled colon segmentation]
+[[File:File.jpg]] | Labelled colon segmentation]
+[[File:File.jpg]]
 ==Target Data Management Process Option B. batch scripted upload via DICOM Server (Yong Gao) '''CURRENTLY BEING DEVELOPED'''==
 * Create new project using web GUI
@@ Line 300: / Line 300: @@
 <br>
 '''6. Confirm''' data is uploaded & represented properly with web GUI

@@ Line 55: / Line 55: @@
 is in fact unique. Apparently, xnat only checks the first image of a series to check that the SOPInstanceUID is in fact unique as I was
 able to apply the remapper to a series of data with a single .das file that set the same SOPInstanceUID to every image in the series.
-Below are the SOPInstanceUID and SeriesInstanceUID that were applied.
+Below are the SOPInstanceUID and SeriesInstanceUID that were applied to the segmented data:
   (0008,0018) := "1.2.840.113619.2.207.3596.11861984.22869.1219405353.999"
   (0020,000e) := "1.2.840.113619.2.207.3596.11861984.25740.1219404288.477"
 ==Target Data Management Process Option B. batch scripted upload via DICOM Server (Yong Gao) '''CURRENTLY BEING DEVELOPED'''==