TractographyWorkshop Core1 ActionPlan - Revision history

Sylvain: /* Challenges in data processing */

2007-12-17T22:56:01Z

Challenges in data processing

2007-12-16T18:51:56Z

2007-12-13T20:42:46Z

Challenges in data processing

2007-12-13T20:37:00Z

Challenges in data processing

2007-12-13T20:27:20Z

2007-12-12T22:41:03Z

Outcome metrics:

2007-12-04T17:57:16Z

2007-12-04T17:51:47Z

2007-12-04T17:39:03Z

2007-12-04T17:30:29Z

@@ Line 204: / Line 204: @@
 # Image frame and measurement frame not equivalent for tensor data.
 # Several datasets corrupted
-## M87102113_visit1
+## M87102113_visit1 - fixed (Sylvain)
-## M02100023_visit1 and visit2
+## M02100023_visit1 and visit2 - should not be used in study (Sylvain)
-## M52200010_visit1
+## M52200010_visit1 - fixed (Sylvain)
 # ROI origin not the same as tensor data.  workaround: set origin to (0,0,0) in ROI images.

@@ Line 195: / Line 195: @@
 Please list below any challenges that you encounter in processing the data.
-# Automatic mask generation failed for provided tensors.  workaround: Reestimating tensors with fixed threshold or masking out outlier DWI intensities.
+# Automatic mask generation, threshold detection failed for provided tensors.  workaround: Reestimate tensors with fixed threshold.
 # Image frame and measurement frame not equivalent for tensor data.
-# Several Datasets corrupted
+# Several datasets corrupted
 ## M87102113_visit1
 ## M02100023_visit1 and visit2

@@ Line 199: / Line 199: @@
 # Several Datasets corrupted
 ## M87102113_visit1
-## M02100023_visit1 or visit2
+## M02100023_visit1 and visit2
 ## M52200010_visit1
 # ROI origin not the same as tensor data.  workaround: set origin to (0,0,0) in ROI images.

@@ Line 191: / Line 191: @@
 )  Each group will be responsible for implementing their own algorithm starting at whatever point in this stream is appropriate for their software.  All agreed NOT to use alternate methods to accomplish any of the afore listed steps.<br />
 <br />
 == Outcome metrics: ==

@@ Line 196: / Line 196: @@
 This is still under discussion, but for the next round of presentations at the January All Hands meeting we agreed to do the following:<br />
 ) Everyone will email Sonia Pujol their slides from the Santa Fe meeting and she and I will use them to compile an Excel worksheet for each laboratory to fill in as they process the new dataset.  This will include information such as: <br />
-a)  Space carved (Casey's DTIprocess tool that generates a volume label map measure from traceline).  This will give volumes, overlap, mean and Std Dev of FA, trace, mode.  We will use these for test-retest metrics.  Each group will pass these label maps to Sonia and she will generate these measures for the AHM presentation.  <br />
+a)  Space carved (Casey's [http://www.sci.utah.edu/~gcasey/research/code DTIprocess] tool that generates a volume label map measure from traceline).  This will give volumes, overlap, mean and Std Dev of FA, trace, mode.  We will use these for test-retest metrics.  Each group will pass these label maps to Sonia and she will generate these measures for the AHM presentation.  <br />
 b) User interface, hardware/software (processor speed, platform, RAM), operator time<br />
 c) Parameter settings for each algorithm<br />

@@ Line 82: / Line 82: @@
 <code>M02100023_visit1.tar.gz</code><br>
 <code>M02100023_visit2.tar.gz</code><br>
 case M02100024

← Older revision		Revision as of 17:51, 4 December 2007
Line 204:		Line 204:
	Further discussion of how best to parameterize tracts will be a key point for the January AHM<br />		Further discussion of how best to parameterize tracts will be a key point for the January AHM<br />

		+
		+	===Uploading your results===
		+
		+	The following directory has been created on the SRB for uploading your results<br />
		+
		+	/home/Projects/NAMIC_DTI_VALIDITY__0074/Results<br />
		+
		+	The below example assumes that you have the SRB Scommands installed and configured for a user that is a member of the NAMIC_DTI_VALIDITY__0074 group<br />
		+
		+	<code>Scd /home/Projects/NAMIC_DTI_VALIDITY__0074/Results</code><br />
		+	<code>Smkdir MyTestResultsDir</code><br />
		+	<code>Schmod a NAMIC_DTI_VALIDITY__0074 groups MyTestResultsDir</code><br />
		+	<code>Scd MyTestResultsDir</code><br />
		+	<code>Sput MyTestFile .</code><br />
		+	<code>Schmod a NAMIC_DTI_VALIDITY__0074 groups MyTestFile</code><br />
		+	<br />

	<br />		<br />

@@ Line 36: / Line 36: @@
-{| class="wikitable"
+{| border="1"
 |-
 ! FileName

← Older revision		Revision as of 17:30, 4 December 2007
Line 34:		Line 34:
	* the tar.gz archive contains the initial raw data,		* the tar.gz archive contains the initial raw data,
	* the tgz archive contains the pre-processed data (Eddy current and EPI correction).		* the tgz archive contains the pre-processed data (Eddy current and EPI correction).
		+
		+
		+	{\| class="wikitable"
		+	\|-
		+	! FileName
		+	! Description
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_dti-Ed-Epi.nhdr
		+	\| Eddy current corrected, EPI corrected and weighted least square estimation diffusion tensor
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_dwi-Ed-Epi.nhdr
		+	\| Eddy current corrected and EPI corrected dwi
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_dti-Ed.nhdr
		+	\| Eddy current corrected and weighted least square estimation diffusion tensor
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_dwi-Ed.nhdr
		+	\| Eddy current corrected dwi
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_dwi.nhdr
		+	\| Raw dwi
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_fieldmag1.nhdr
		+	\| Field Map used for EPI correction.
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_fieldmag2.nhdr
		+	\|
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_fieldphase1.nhdr
		+	\|
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_fieldphase2.nhdr
		+	\|
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_t1.nhdr
		+	\| t1 weighted scan
		+	\|-
		+	\| M02100024_visit1/M02100024_visit1_t2.nhdr
		+	\| t2 weighted scan
		+	\|}
		+