July31T-con/Synopsis - Revision history

RandyGollub at 17:41, 9 August 2007

2007-08-09T17:41:46Z

RandyGollub at 17:41, 9 August 2007

2007-08-09T17:41:04Z

RandyGollub at 17:37, 9 August 2007

2007-08-09T17:37:44Z

RandyGollub at 17:30, 9 August 2007

2007-08-09T17:30:45Z

RandyGollub at 04:43, 9 August 2007

2007-08-09T04:43:47Z

RandyGollub at 04:42, 9 August 2007

2007-08-09T04:42:10Z

RandyGollub at 04:36, 9 August 2007

2007-08-09T04:36:53Z

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RandyGollub at 03:47, 9 August 2007

2007-08-09T03:47:27Z

RandyGollub at 03:33, 9 August 2007

2007-08-09T03:33:59Z

RandyGollub at 03:23, 9 August 2007

2007-08-09T03:23:47Z

@@ Line 25: / Line 25: @@
 * Outstanding questions:
 # What is the b value of the scans?
 <br>

@@ Line 11: / Line 11: @@
 <br>
 '''3. Proposed Solution''' <br>
-To cut to the chase: We should post 3 data sets.  The "raw" data is uploaded now.   Marc Niethammer will prepare and upload isotropic down sampled data, ROIs and computed tensors.  He will provide a clear detailed description of what exactly he does as part of the upload, but see email trail below for his proposal.  Those groups that want to work with upsampled isotropic data will generate their own upsampled data sets from the raw data and will include that step in their slide presentation as part of their processing methods.  We will discuss in Sante Fe whether we should post the data and the resampled ROIs for the others to use.
+To cut to the chase: We will post 2 data sets.  The "raw" data is uploaded now.   Marc Niethammer will prepare and upload isotropic down sampled data, ROIs and computed tensors.  He will provide a clear detailed description of what exactly he does as part of the upload, but see email trail below for his proposal.  Those groups that want to work with upsampled isotropic data will generate their own upsampled data sets from the raw data and will include that step in their slide presentation as part of their processing methods.  We will discuss in Sante Fe whether we should post the data and the resampled ROIs for the others to use.  If you want to also use the eddy current corrected data and then show quantitatively the improvement then do so using the raw data.
 <br>
 <br>

@@ Line 11: / Line 11: @@
 <br>
 '''3. Proposed Solution''' <br>
-To cut to the chase: We should post 3 data sets.  The "raw" data is uploaded now.   Marc Niethammer will prepare and upload isotropic down sampled data, ROIs and computed tensors.  He will provide a clear detailed description of what exactly he does as part of the upload.  Those groups that want to work with upsampled isotropic data  - gather yourselves and chose who is going to do the interpolation and post the data and the resampled ROIs for the others to use.
+To cut to the chase: We should post 3 data sets.  The "raw" data is uploaded now.   Marc Niethammer will prepare and upload isotropic down sampled data, ROIs and computed tensors.  He will provide a clear detailed description of what exactly he does as part of the upload, but see email trail below for his proposal.  Those groups that want to work with upsampled isotropic data will generate their own upsampled data sets from the raw data and will include that step in their slide presentation as part of their processing methods.  We will discuss in Sante Fe whether we should post the data and the resampled ROIs for the others to use.
 <br>
 <br>
 '''1. New Information- Key points extracted from the discussion below''' <br>
-* The wiki has been edited to correct the image acquisition details.  The data were collected on a GE scanner using parallel imaging.  The prescribed slice resolution is not what is actually written in the "raw" image file as provided by GE.  There is some proprietary preprocessing done as or after the data are taken out of K-space and before the non-linear combination of the parallel images.  The data available on the scanner has a resolution of 0.9x0.9x1.7mm (no gap), FOV 240 x 240.  That data is the closest to "raw" that is available and is what is currently posted as '''dwi'''.  The ROIs were generated at this resolution.
+* The wiki has been edited to correct the image acquisition details.  The data were collected on a GE scanner using parallel imaging.  The prescribed slice resolution is not what is actually written in the "raw" image file as provided by GE.  There is some proprietary preprocessing done as or after the data are taken out of K-space and before the non-linear combination of the parallel images.  The data available on the scanner has a resolution of 0.9375 x0.9375 x1.7mm (no gap), FOV 240 x 240.  That data is the closest to "raw" that is available and is what is currently posted as '''dwi'''.  The ROIs were generated at this resolution.
 * There are three camps within our small group, those whose algorithms can work with this data "as is", those who need upsampled isotropic voxels and those who need downsampled isotropic voxels.
 * The '''dwi-EdCor''' files are the "raw" data that have been corrected for eddy currents using an FSL tool to do an affine registration of each dwi to the first baseline.
@@ Line 23: / Line 23: @@
 * Marek provided the requested information required for clinical relevance of this project WRT the choices of tracts and potential hypotheses to be tested.  I have edited them into the ROI page and our Project Page.
 * Per Stephan Aylward, Core 2 engineers are interested in helping us to post our final results and/or any other material we wish to share with the scientific community.   The top-level website for the effort is http://insight-journal.org/nlm/
 <br>

@@ Line 11: / Line 11: @@
 <br>
 '''3. Proposed Solution''' <br>
-To cut to the chase: We should post 3 data sets.  The "raw" data is uploaded now.  Those groups that want to work with upsampled data- gather yourselves and chose who is going to do the interpolation and post the data and the resampled ROIs for the others to use.  Same thing for the groups who want to use down sampled data.
+To cut to the chase: We should post 3 data sets.  The "raw" data is uploaded now.   Marc Niethammer will prepare and upload isotropic down sampled data, ROIs and computed tensors.  He will provide a clear detailed description of what exactly he does as part of the upload.  Those groups that want to work with upsampled isotropic data  - gather yourselves and chose who is going to do the interpolation and post the data and the resampled ROIs for the others to use.
 <br>
 <br>

@@ Line 240: / Line 240: @@
 Hi Everyone,
 This may have been resolved already on traffic that I haven't
 seen, but was there, in fact, a slice gap in this data?  That seems
 a little odd for DTI data that you're going to use to generate
@@ Line 291: / Line 290: @@
 Hi Marc,
 So you essentially re-zero-filled already zero-filled data and
 then did the IFT back into the zero-filled matrix size.  Did you
 try putting the LP-filtered data into a 144 x 144 matrix

@@ Line 1: / Line 1: @@
 == Each of the algorithms has an optimal voxel dimension and they are not the same.  We must decide what format of the data will be used as the common starting point. ==
   <br>
@@ Line 12: / Line 13: @@
 <br>
 '''1. New Information''' <br>
-* The wiki has been edited to correct the image acquisition details.  The data were collected on a GE scanner using parallel imaging.  The prescribed slice resolution of x is not what is actually in the raw image file as reconstructed by GE.  There is some proprietary preprocessing done as or after the data are taken out of K-space and before the non-linear combination of the parallel images.  The data available on the scanner has a resolution of y.  That data is the closest to "raw" that is available and is what is currently posted.  The ROIs were generated at this resolution.
+* The wiki has been edited to correct the image acquisition details.  The data were collected on a GE scanner using parallel imaging.  The prescribed slice resolution of x is not what is actually in the raw image file as reconstructed by GE.  There is some proprietary preprocessing done as or after the data are taken out of K-space and before the non-linear combination of the parallel images.  The data available on the scanner has a resolution of 0.9x0.9x1.7mm (no gap), FOV 240 x 240, 256 x 256.  That data is the closest to "raw" that is available and is what is currently posted as '''dwi'''.  The ROIs were generated at this resolution.
 * There are three camps within our small group, those whose algorithms can work with this data "as is", those who need upsampled isotropic voxels and those who need downsampled isotropic voxels.
 From Guido on August 6:
@@ Line 63: / Line 106: @@
 -Sylvain
 Return to [[July31T-con | July31T-con Page]]

← Older revision		Revision as of 03:33, 9 August 2007
Line 1:		Line 1:
−	== The Problem: <br>	+	== The Problem: == <br>
−	~~Each of the algorithms has an optimal voxel dimension and they are not the same. We must decide what format of the data will be used as the common starting point. ==~~

		+	== Each of the algorithms has an optimal voxel dimension and they are not the same. We must decide what format of the data will be used as the common starting point. ==
		+	<br>

−	I have three goals here, 1) to summarize the new information gained during the past 9 days since we had our T-con, 2) to capture the essence of the discussions that took place in pursuit of that information and 3) to propose a final solution regarding the format of the starting data to be processed by all the groups for the Santa Fe meeting that will be a reasonable compromise between the in principle optimal but completely impossible solution of all groups using the "same data" and the "every group for themselves" solution that will require more work in Sante Fe to sort out our results.

		+	I have three goals here:
		+	# to summarize the new information gained during the past 9 days since we had our T-con <br>
		+	# to capture the essence of the discussions that took place in pursuit of that information and <br>
		+	# to propose a final solution regarding the format of the starting data to be processed by all the groups for the Santa Fe meeting that will be a reasonable compromise between the in principle optimal but completely impossible solution of all groups using the "same data" and the "every group for themselves" solution that will require more work in Sante Fe to sort out our results.

		+	<br>
		+	'''1. New Information''' <br>
		+	* The wiki has been edited to correct the image acquisition details. The data were collected on a GE scanner using parallel imaging. The prescribed slice resolution of x is not what is actually in the raw image file as reconstructed by GE. There is some proprietary preprocessing done as or after the data are taken out of K-space and before the non-linear combination of the parallel images. The data available on the scanner has a resolution of y. That data is the closest to "raw" that is available and is what is currently posted. The ROIs were generated at this resolution.
		+	* There are three camps within our small group, those whose algorithms can work with this data "as is", those who need upsampled isotropic voxels and those who need downsampled isotropic voxels.

	From Guido on August 6:		From Guido on August 6:

← Older revision		Revision as of 03:23, 9 August 2007
Line 1:		Line 1:
−		+	== The Problem: <br>
−	== The Problem: Each of the algorithms has an optimal voxel dimension and they are not the same. We must decide what format of the data will be used as the common starting point. ==	+	Each of the algorithms has an optimal voxel dimension and they are not the same. We must decide what format of the data will be used as the common starting point. ==