DTI Validation Telephone Conferences 2008 - Revision history

RandyGollub at 16:06, 22 April 2008

2008-04-22T16:06:51Z

RandyGollub at 16:06, 22 April 2008

2008-04-22T16:06:26Z

RandyGollub at 15:41, 1 April 2008

2008-04-01T15:41:25Z

RandyGollub at 15:39, 1 April 2008

2008-04-01T15:39:16Z

RandyGollub at 17:00, 18 March 2008

2008-03-18T17:00:27Z

RandyGollub at 16:59, 18 March 2008

2008-03-18T16:59:33Z

RandyGollub at 19:02, 4 March 2008

2008-03-04T19:02:27Z

RandyGollub at 19:01, 4 March 2008

2008-03-04T19:01:21Z

RandyGollub: /* '''ACTION PLANS''': */

2008-03-04T19:00:42Z

'''ACTION PLANS''':

RandyGollub at 17:03, 4 March 2008

2008-03-04T17:03:39Z

@@ Line 21: / Line 21: @@
 '''ACTION PLANS'''
 # C.-F. and John to work collaboratively to enable GA Tech to share the matlab code and TEEM libraries for running their Volumetric tractography algorithm here at BWH
 # Next T-con is Tuesday May 13, 2008 - 11:00 am EST

← Older revision		Revision as of 16:06, 22 April 2008
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		+	'''Tuesday April 22, 2008 - 11:00 am EST'''
		+
		+	'''PROGRESS:'''
		+	*MIND DATA<br/>
		+	The MIND data will be completely re-processed and uploaded by the end of this week. Then Sonia will verify and make any necessary corrections to the ROIs.
		+
		+	*PHANTOM DATA<br/>
		+	The GA Tech group has converted their results to vtkPolydata format and put them into the SRB repository along with the previous nrrd format results.
		+
		+	The GA Tech site's Volume Tractography algorithm is undergoing another round of improvements and is starting to show good results now. Thus the currently generated results from that site should be considered preliminary and they plan to redo the analysis once the algorithm is once again in a stable state. They commented favorably on the utility of this project for testing their algorithm and giving them insights for how to make improvements.
		+
		+	Still waiting to for Casey, Tri and Nathan to post their TEEM phantom results on the SRB. Please just email the results to Sonia, she will get them posted and integrate them into the cross site analysis she has underway as soon as she gets them from you.
		+
		+	*OTHER<br/>
		+	Steve Pieper briefly summarized the current status of Slicer 3 DTI processing for us. See this link for details http://www.na-mic.org/Wiki/index.php/Slicer3:DTMRI.
		+
		+	Carlo Pierpoli joined the meeting to hear the update on Slicer 3 and to discuss a potential future presentation on DTI analysis algorithms for the 2009 ISMRM. He will work with C.F. as the NAMIC point person to discuss further when both are at the 2008 ISMRM.
		+
		+	Jim Fallon sent a package with the drawn "gold standard" neural pathways we are seeking to use DTI to segment to Sonia, but we have not yet received it yet. We are working to find the package and/or he will resend. (THANKS JIM!!!)
		+
		+	'''ACTION PLANS'''
		+	# C.-F. and John to work collaboratively to enable GA Tech to share the matlab code and TEEM libraries for running their Volumetric tractography algorithm here at BWH
		+
		+	# Next T-con is Tuesday May 13, 2008 - 11:00 am EST
		+
		+
	'''Tuesday April 1, 2008 - 11:00 am EST'''		'''Tuesday April 1, 2008 - 11:00 am EST'''

@@ Line 7: / Line 7: @@
 *PHANTOM DATA<br/>
-Two weeks ago Casey, Tri and Nathan (in an email to Randy) reported successfully generating tracts from the TEEM phantom but they have not yet posted them on the SRB.  Please just email the results to Sonia, she will get them posted and begin the cross site analysis as soon as she gets them from you.  John also obtained results, but isn't happy with results- the algorithm "hugs the inner curvature" of the helix.  He is working with a new phantom that he made that is more suited for his algorithm.  Discussed value of sharing vtkPolydata results from TEEM phantom, John will show Vandana how to do this.
+Two weeks ago Casey, Tri and Nathan (in an email to Randy) reported successfully generating tracts from the TEEM phantom but they have not yet posted them on the SRB.  Please just email the results to Sonia, she will get them posted and integrate them into the cross site analysis she has underway as soon as she gets them from you.  John also obtained results, but isn't happy with results- the algorithm "hugs the inner curvature" of the helix.  He is working with a new phantom that he made that is more suited for his algorithm.  Discussed value of sharing vtkPolydata results from TEEM phantom, John will show Vandana how to do this.
 *OTHER<br/>
@@ Line 16: / Line 16: @@
 '''ACTION PLANS'''
 # Process TEEM phantom data and email Sonia your results in vtkPolydata format
 # Don't work on the MIND data until we notify you that the correct data is posted and ready for download.
 # Next T-con is Tuesday April 22, 2008 - 11:00 am EST; NOTE PUSHED BACK ONE WEEK

← Older revision		Revision as of 15:39, 1 April 2008
Line 1:		Line 1:
−	'''Tuesday March 18, 2008 - 11:00 am EST'''	+	'''Tuesday April 1, 2008 - 11:00 am EST'''
		+
		+
		+	'''PROGRESS:'''
		+	*MIND DATA<br/>
		+	We are still waiting for Jeremy/MIND team to redo the whole cohort and upload the data, replacing the incorrect files on the SRB.
		+
		+	*PHANTOM DATA<br/>
		+	Two weeks ago Casey, Tri and Nathan (in an email to Randy) reported successfully generating tracts from the TEEM phantom but they have not yet posted them on the SRB. Please just email the results to Sonia, she will get them posted and begin the cross site analysis as soon as she gets them from you. John also obtained results, but isn't happy with results- the algorithm "hugs the inner curvature" of the helix. He is working with a new phantom that he made that is more suited for his algorithm. Discussed value of sharing vtkPolydata results from TEEM phantom, John will show Vandana how to do this.
		+
		+	*OTHER<br/>
		+	CF briefly summarized results of Core 1 meeting in SLC March 24-26. See this link for details http://www.na-mic.org/Wiki/index.php/2008_Engineering_review_at_Utah:Summary.
		+
		+	Proceeding with plans for Randy, CF and Sonia to co-mentor a MIT summer student to assist with data analysis, project integration and presentation of results.
		+
		+	'''ACTION PLANS'''
		+	# Process TEEM phantom data and email Sonia your results in vtkPolydata format
		+	# Don't work on the MIND data until we notify you that the correct data is posted and ready for download.
		+	# Next T-con is Tuesday April 22, 2008 - 11:00 am EST; NOTE PUSHED BACK ONE WEEK
		+
		+
		+	'''Tuesday March 18th, 2008 - 11:00 am EST'''

@@ Line 16: / Line 16: @@
 '''ACTION PLANS'''
 #All groups need to finish processing the TEEM helix data and post tracts file in VTKPolydata format on SRB by next T-con (sound familiar?).  Next T-con is April Fool's Day.
-# Wait to continue work on the MIND data until we notify you that the correct data is posted and ready for download.
+# Don't work on the MIND data until we notify you that the correct data is posted and ready for download.

← Older revision		Revision as of 16:59, 18 March 2008
Line 1:		Line 1:
		+	'''Tuesday March 18, 2008 - 11:00 am EST'''
		+
		+
		+	'''PROGRESS:'''
		+	*MIND DATA<br/>
		+	Sonia has fixed the scripts that convert the Siemens DICOM image data to nrrd format. She is passing the scripts to Jeremy who will redo the whole cohort and upload the data, replacing the incorrect files on the SRB by the end of this week.
		+
		+	*PHANTOM DATA<br/>
		+	Casey, Tri and Nathan (in an email to Randy) reported successfully generating tracts from the TEEM phantom and are working to post them on the SRB. See email from Jeremy regarding changes due to the SRB upgrades that have recently taken place.
		+
		+	*OTHER<br/>
		+	Discussed integration of tractography algorithms into the Slicer 3 environment as a way to facilitate forward progress. Ross, Guido, CF, Casey, Steve, and others will be meeting in SLC March 24-26 and this will be one of the agenda items. We are all eager to see this happen.
		+
		+	Suggestion to consolidate analysis of data from multiple algorithms (in or out of Slicer3) at a single site (BWH hosting) considered by the group. Randy offered to sponsor from Training Core funds a summer student to assist with data analysis, project integration and presentation of results.
		+
		+	'''ACTION PLANS'''
		+	#All groups need to finish processing the TEEM helix data and post tracts file in VTKPolydata format on SRB by next T-con (sound familiar?). Next T-con is April Fool's Day.
		+	# Wait to continue work on the MIND data until we notify you that the correct data is posted and ready for download.
		+
		+
		+
	'''Tuesday March 4, 2008 - 11:00 am EST'''		'''Tuesday March 4, 2008 - 11:00 am EST'''

@@ Line 21: / Line 21: @@
 '''PROGRESS:'''
-Tri's phantom data was downloaded by a few groups who were able to generate tracts from it.  No problems were encountered, but not all groups have yet attempted it.  I believe that all sites have now uploaded results for the one subject we agreed to do for the AHM meeting.  Sylvain Gouttard found an error in the ROIs posted for generating the arcuate fasiculus tract, so please disregard that until Sonia posts a corrected set of ROIs and sends out an email notice.  Nathan was not on call and no input on what the problems are with his phantom.
+The TEEM phantom data was downloaded by a few groups who were able to generate tracts from it.  No problems were encountered, but not all groups have yet attempted it.  I believe that all sites have now uploaded results for the one subject we agreed to do for the AHM meeting.  Sylvain Gouttard found an error in the ROIs posted for generating the arcuate fasiculus tract, so please disregard that until Sonia posts a corrected set of ROIs and sends out an email notice.  Nathan was not on call and no input on what the problems are with his phantom.
 == '''ACTION PLANS''':  ==

@@ Line 6: / Line 6: @@
 Sonia has identified that the initial script run in New Mexico to start the conversion of the DWI DICOM mosaic data to nrrd format erroneously cut 4 slices of the image data away.  This is what resulted in the misregistration with the Freesurfer segmentation data and the created the problem with the acruate fasciculus ROIs.  This good to know before we get any further so we can verify that this error did not affect the brain and report back next meeting. She will need to redo the ROIs so don't work on this part of the project yet.   Jim Fallon is creating the "master neuroanatomist" hand segmentation of the tracts we are using for this project.  (Awesome JIM!)
 *PHANTOM DATA<br/>
-Sonia posted Slicer tractography results from Tri's phantom (see figure below).  John M downloaded and began processing the phantom data, but is noting some issues due to the large homogenous volume of the synthetic tract (e.g. follows inner curve of helix).  He would like to work with it more and will report results at next T-con.  Nothing from any other site.  MICCAI and other deadlines have been a major time constraint.  Discussed options for how to motivate forward progress on project, with CF suggesting more frequent email reminders and use of the wiki to document individual site progress.
+Sonia posted Slicer tractography results from the TEEM phantom (see figure below).  John M downloaded and began processing the phantom data, but is noting some issues due to the large homogenous volume of the synthetic tract (e.g. follows inner curve of helix).  He would like to work with it more and will report results at next T-con.  Nothing from any other site.  MICCAI and other deadlines have been a major time constraint.  Discussed options for how to motivate forward progress on project, with CF suggesting more frequent email reminders and use of the wiki to document individual site progress.
 *OTHER<br/>
 Randy described another approach to validating DTI tractography used by Martinos colleagues.  She will circulate the 2005 ISMRM abstract and associated website information to the group for future discussion.

@@ Line 24: / Line 24: @@
 == '''ACTION PLANS''':  ==
-#All sites PLEASE download Tri's new phantom data (in nrrd format w/ROIs) ASAP and run your tractography algorithm on it, and upload your results (tract fields and matricies) before next T-con (Tuesday March 4th).
+#All sites PLEASE download new TEEM phantom data (in nrrd format w/ROIs) ASAP and run your tractography algorithm on it, and upload your results (tract fields and matricies) before next T-con (Tuesday March 4th).
 # All sites look at the results of the registration between the DTI data and structural scan for the exemplar subject (and as many as you have time for) so we can discuss any outstanding registration issues (brought up as a potential problem by Guido).
@@ Line 51: / Line 51: @@
 * Randy will update the wiki to add this info to our ROI page.
 [[Image:TeemPhantom-SlicerROI0001.png | 250 px | right]]
 == '''ACTION PLANS''':  ==
 #All sites download Tri's new phantom data (in nrrd format w/ROIs) ASAP and run your tractography algorithm on it, and upload your results (tract fields and matricies) before next Tuesday's T-con (Tuesday Feb. 19th).

@@ Line 11: / Line 11: @@
 <br/>
 '''ACTION PLANS'''
-Sonia will set up a wiki progress page for us and email everyone when it is ready.  Randy will send first reminder to group right after MICCAI deadline. All groups need to process the TEEM helix data and post results by next T-con on March 18th.
+#All groups need to process the TEEM helix data and post results by next T-con on March 18th