Difference between revisions of "Oct 08 2009 meeting: schedule for Oct 9"
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With Ron: | With Ron: | ||
| − | * what caused the hole in Valentino data | + | * what caused the hole in Valentino data? Ron: the impression is that this is a cyst |
| − | * check the quality of N3 bias correction | + | * check the quality of N3 bias correction. Ron: recovered bias field makes sense. |
| − | * learn how to manually segment sub-cortical structures | + | * learn how to manually segment sub-cortical structures -- need 3-class segmentation to do this, not ready yet |
With Sandy: | With Sandy: | ||
| Line 13: | Line 13: | ||
* workflow -- how much benefit we can expect if we make it more complex, is it worth it (e.g., do EM segment on each subject, then re-run atlas construction without bias field, considering there is improvement) | * workflow -- how much benefit we can expect if we make it more complex, is it worth it (e.g., do EM segment on each subject, then re-run atlas construction without bias field, considering there is improvement) | ||
| − | * can we think of quantitative criterion for bias correction with N3? -- we could script and run parameter exploration | + | * can we think of quantitative criterion for bias correction with N3? -- we could script and run parameter exploration. Sandy: can possibly check the result by running classification, compute gaussians for each class, and calculate classification error as a metric. |
| − | * check the quality of the smoothed data | + | * check the quality of the smoothed data. Sandy: run EM on the non-smoothed data, because boundaries may have been affected, and MF should take care of Gaussian noise. |
With Chris: | With Chris: | ||
| − | * information about the second timepoint data / data transfer issue | + | * information about the second timepoint data / data transfer issue. Data transfered. Verified image quality for the second time point -- not better than the first one, based on Calvin images. |
| − | * confirm there are no intellectual property issues for the workflow tools originating from VT -- can we put everything in NA-MIC sandbox to maximize reuse later? | + | * confirm there are no intellectual property issues for the workflow tools originating from VT -- can we put everything in NA-MIC sandbox to maximize reuse later? Confirmed |
With all: | With all: | ||
| − | * look at the current results of the initial registration (up to affine) | + | * look at the current results of the initial registration (up to affine) -- Registraton ok, but Tommy is not a good template candidate (motion and susceptibility artifacts; head shape not normal, possibly to premature birth). Switch to Gucci. |
* build up the list of non-slicer3 tools / scripts, discuss sharing of code and data (data -- after the publication(s) are out) | * build up the list of non-slicer3 tools / scripts, discuss sharing of code and data (data -- after the publication(s) are out) | ||
| Line 31: | Line 31: | ||
* discuss protocols on documentation; | * discuss protocols on documentation; | ||
| − | * conform proposed work flow; | + | * conform proposed work flow; |
| − | * discuss time-line / winter NAMIC meeting/ potential publications. | + | * discuss time-line / winter NAMIC meeting/ potential publications. Confirmed meet Chris and Ginger at SLC. Try to arrange phone call with imaging people before that. |
| + | |||
| + | Some other points: | ||
| + | * consider XNAT for storing raw data | ||
| + | * understand what to expect in the MRS data, discuss with Bjoern Menze | ||
Latest revision as of 13:31, 12 October 2009
Home < Oct 08 2009 meeting: schedule for Oct 9With Ron:
- what caused the hole in Valentino data? Ron: the impression is that this is a cyst
- check the quality of N3 bias correction. Ron: recovered bias field makes sense.
- learn how to manually segment sub-cortical structures -- need 3-class segmentation to do this, not ready yet
With Sandy:
- discuss EM segmenter -- talk with Chris, go through all recommendations for Ginger to take home
- workflow -- how much benefit we can expect if we make it more complex, is it worth it (e.g., do EM segment on each subject, then re-run atlas construction without bias field, considering there is improvement)
- can we think of quantitative criterion for bias correction with N3? -- we could script and run parameter exploration. Sandy: can possibly check the result by running classification, compute gaussians for each class, and calculate classification error as a metric.
- check the quality of the smoothed data. Sandy: run EM on the non-smoothed data, because boundaries may have been affected, and MF should take care of Gaussian noise.
With Chris:
- information about the second timepoint data / data transfer issue. Data transfered. Verified image quality for the second time point -- not better than the first one, based on Calvin images.
- confirm there are no intellectual property issues for the workflow tools originating from VT -- can we put everything in NA-MIC sandbox to maximize reuse later? Confirmed
With all:
- look at the current results of the initial registration (up to affine) -- Registraton ok, but Tommy is not a good template candidate (motion and susceptibility artifacts; head shape not normal, possibly to premature birth). Switch to Gucci.
- build up the list of non-slicer3 tools / scripts, discuss sharing of code and data (data -- after the publication(s) are out)
- discuss protocols on documentation;
- conform proposed work flow;
- discuss time-line / winter NAMIC meeting/ potential publications. Confirmed meet Chris and Ginger at SLC. Try to arrange phone call with imaging people before that.
Some other points:
- consider XNAT for storing raw data
- understand what to expect in the MRS data, discuss with Bjoern Menze
