DBP:Harvard:Software:Minutes:5 - Revision history

Andy: Update from Wiki

2006-12-18T13:55:18Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:55:17Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:55:16Z

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Andy: Update from Wiki

2006-12-18T13:19:22Z

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Andy: Update from Wiki

2006-12-18T13:19:22Z

Update from Wiki

Andy: Update from Wiki

2006-12-18T13:19:21Z

Update from Wiki

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== DTI Meeting Minutes | May 3, 2006 ==

<br /> Present: Marty, CF, Gordon, Mark, Marc, Doug, KangUk, Sylvain, Marek

<br />'''Scanning'''

* Marek is continuing to test out the new sequence
* New rule that a licensed MD must request MRI even if for research
* Problem with reconstruction with multiple b-value images; causing FA to decrease significantly
* At the scanner, unable to arbitrarily decide the number of baseline images; Marek will try to manually change whatever parameter this is
* Can get resolution of scans down to 1.5x1.5x1.5, but this may increase noise in the images

<br />'''Tensor Registration'''

* Goal of this is coregistration of segmented white matter labelmaps with our data
* In test of new tensor registration module from Mattan, linear registration is working better than nonlinear, which is way off
* KangUk will test this with scans of the same resolution
* This registration is done at scalar level, and is not actually using the tensors; we can try the same thing using AG and multiple scalar maps
* Marc will try to troubleshoot this on Friday

<br />'''Anterior Commissure, Mode/FA histograms'''

* Gordon has sent scripts for creating AC boundary maps
* Gordon has sent script for generating histograms; will continue to work on this using labelmaps PNL sends to him.

@@ Line 1: / Line 1: @@
-== DTI Meeting Minutes | May 10, 2006 ==
+== DTI Meeting Minutes | May 31, 2006 ==
-<br /> Present: CF, Marty, Marc, Mark, Toshiro, KangUk, Doug, Sylvain, Gordon
+<br />'''Present:''' Doug, Sylvain, Katharina, Marek, Marty, CF, Toshiro, KangUk
-<br />'''New Sequence:'''
+<br />'''Tensor Coregistration:'''
-* Nan-kuei will be helping with testing of the new sequence
+* Usman is working on coregistration for KangUk; each case takes about 3 hours to process
-* Once sequence is decided, planning on bringing in all previous DTI subjects during month of July
+* Mattan has improved his method; KangUk will test the update to see if it is faster or more accurate than the current method through Slicer
-* Test images
+* Soon the TransformVolume module in Slicer will be able to resample tensor datasets
-** 1.7^3 resolution
+* Reminder that KangUk is leaving at the end of August
-<br />'''KangUk - White matter atlas coregistration:'''
+<br />'''Anterior Commissure:'''
-* Both linear and nonlinear coregistration still not that great for a problematic case
+* Sylvain created ColorByOrientation maps, but Gordon's boundaries are not matching well, perhaps due to some interpolation issue; Sylvain and Gordon will work on this
-<br />'''DTMRI scalar testing:'''
+<br />'''DeLisi data:'''
-* Needs to be an estimation error map in the pipeline; but this is sequence-dependent, so will have not be implemented until new sequence is set
+* Originally wanted to trace cingulate, uncinate, and fornix

@@ Line 1: / Line 1: @@
-== DTI Meeting Minutes | May 3, 2006 ==
+== DTI Meeting Minutes | May 10, 2006 ==
-<br /> Present: Marty, CF, Gordon, Mark, Marc, Doug, KangUk, Sylvain, Marek
+<br /> Present: CF, Marty, Marc, Mark, Toshiro, KangUk, Doug, Sylvain, Gordon
-<br />'''Scanning'''
+<br />'''New Sequence:'''
-* Marek is continuing to test out the new sequence
+* Nan-kuei will be helping with testing of the new sequence
-* New rule that a licensed MD must request MRI even if for research
+* Once sequence is decided, planning on bringing in all previous DTI subjects during month of July
-* Problem with reconstruction with multiple b-value images; causing FA to decrease significantly
+* Test images
-* At the scanner, unable to arbitrarily decide the number of baseline images; Marek will try to manually change whatever parameter this is
+** 1.7^3 resolution
-* Can get resolution of scans down to 1.5x1.5x1.5, but this may increase noise in the images
+** Problem with a missing DWI for one slice--causes major differences in tensor estimation
-<br />'''Tensor Registration'''
+<br />'''KangUk - White matter atlas coregistration:'''
-* Goal of this is coregistration of segmented white matter labelmaps with our data
+* Both linear and nonlinear coregistration still not that great for a problematic case
-* In test of new tensor registration module from Mattan, linear registration is working better than nonlinear, which is way off
+* KangUk will test on a better case; will try to do dual-channel coregistration in AG using FA and Mode
-* KangUk will test this with scans of the same resolution
+* Will continue to use scalar maps for coregistration; using structural would add an additional registration step and more error
-<br />'''Anterior Commissure, Mode/FA histograms'''
+<br />'''DTMRI scalar testing:'''
-* Gordon has sent scripts for creating AC boundary maps
+* Needs to be an estimation error map in the pipeline; but this is sequence-dependent, so will have not be implemented until new sequence is set

@@ Line 1: / Line 1: @@
-== DTI Meeting Minutes | May 31, 2006 ==
+== DTI Meeting Minutes | May 3, 2006 ==
-<br />'''Present:''' Doug, Sylvain, Katharina, Marek, Marty, CF, Toshiro, KangUk
+<br /> Present: Marty, CF, Gordon, Mark, Marc, Doug, KangUk, Sylvain, Marek
-<br />'''Tensor Coregistration:'''
+<br />'''Scanning'''
-* Usman is working on coregistration for KangUk; each case takes about 3 hours to process
+* Marek is continuing to test out the new sequence
-* Mattan has improved his method; KangUk will test the update to see if it is faster or more accurate than the current method through Slicer
+* New rule that a licensed MD must request MRI even if for research
-* Soon the TransformVolume module in Slicer will be able to resample tensor datasets
+* Problem with reconstruction with multiple b-value images; causing FA to decrease significantly
-* Reminder that KangUk is leaving at the end of August
+* At the scanner, unable to arbitrarily decide the number of baseline images; Marek will try to manually change whatever parameter this is
-<br />'''Anterior Commissure:'''
+<br />'''Tensor Registration'''
-* Sylvain created ColorByOrientation maps, but Gordon's boundaries are not matching well, perhaps due to some interpolation issue; Sylvain and Gordon will work on this
+* Goal of this is coregistration of segmented white matter labelmaps with our data
-<br />'''DeLisi data:'''
+<br />'''Anterior Commissure, Mode/FA histograms'''
-* Originally wanted to trace cingulate, uncinate, and fornix
+* Gordon has sent scripts for creating AC boundary maps
-* Sylvain and Doug will meet to decide how to delineate the cingulate
+* Gordon has sent script for generating histograms; will continue to work on this using labelmaps PNL sends to him.

@@ Line 1: / Line 1: @@
-== DTI Meeting Minutes | May 10, 2006 ==
+== DTI Meeting Minutes | May 31, 2006 ==
-<br /> Present: CF, Marty, Marc, Mark, Toshiro, KangUk, Doug, Sylvain, Gordon
+<br />'''Present:''' Doug, Sylvain, Katharina, Marek, Marty, CF, Toshiro, KangUk
-<br />'''New Sequence:'''
+<br />'''Tensor Coregistration:'''
-* Nan-kuei will be helping with testing of the new sequence
+* Usman is working on coregistration for KangUk; each case takes about 3 hours to process
-* Once sequence is decided, planning on bringing in all previous DTI subjects during month of July
+* Mattan has improved his method; KangUk will test the update to see if it is faster or more accurate than the current method through Slicer
-* Test images
+* Soon the TransformVolume module in Slicer will be able to resample tensor datasets
-** 1.7^3 resolution
+* Reminder that KangUk is leaving at the end of August
-<br />'''KangUk - White matter atlas coregistration:'''
+<br />'''Anterior Commissure:'''
-* Both linear and nonlinear coregistration still not that great for a problematic case
+* Sylvain created ColorByOrientation maps, but Gordon's boundaries are not matching well, perhaps due to some interpolation issue; Sylvain and Gordon will work on this
-<br />'''DTMRI scalar testing:'''
+<br />'''DeLisi data:'''
-* Needs to be an estimation error map in the pipeline; but this is sequence-dependent, so will have not be implemented until new sequence is set
+* Originally wanted to trace cingulate, uncinate, and fornix

@@ Line 1: / Line 1: @@
-== DTI Meeting Minutes | May 3, 2006 ==
+== DTI Meeting Minutes | May 10, 2006 ==
-<br /> Present: Marty, CF, Gordon, Mark, Marc, Doug, KangUk, Sylvain, Marek
+<br /> Present: CF, Marty, Marc, Mark, Toshiro, KangUk, Doug, Sylvain, Gordon
-<br />'''Scanning'''
+<br />'''New Sequence:'''
-* Marek is continuing to test out the new sequence
+* Nan-kuei will be helping with testing of the new sequence
-* New rule that a licensed MD must request MRI even if for research
+* Once sequence is decided, planning on bringing in all previous DTI subjects during month of July
-* Problem with reconstruction with multiple b-value images; causing FA to decrease significantly
+* Test images
-* At the scanner, unable to arbitrarily decide the number of baseline images; Marek will try to manually change whatever parameter this is
+** 1.7^3 resolution
-* Can get resolution of scans down to 1.5x1.5x1.5, but this may increase noise in the images
+** Problem with a missing DWI for one slice--causes major differences in tensor estimation
-<br />'''Tensor Registration'''
+<br />'''KangUk - White matter atlas coregistration:'''
-* Goal of this is coregistration of segmented white matter labelmaps with our data
+* Both linear and nonlinear coregistration still not that great for a problematic case
-* In test of new tensor registration module from Mattan, linear registration is working better than nonlinear, which is way off
+* KangUk will test on a better case; will try to do dual-channel coregistration in AG using FA and Mode
-* KangUk will test this with scans of the same resolution
+* Will continue to use scalar maps for coregistration; using structural would add an additional registration step and more error
-<br />'''Anterior Commissure, Mode/FA histograms'''
+<br />'''DTMRI scalar testing:'''
-* Gordon has sent scripts for creating AC boundary maps
+* Needs to be an estimation error map in the pipeline; but this is sequence-dependent, so will have not be implemented until new sequence is set