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== Countdown == Feb 1 was 8 days ago. :( |
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| * Make available open-source Freesurfer code (minus Numerical Recipes for C code) | |
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| * Updated documentation (wiki) | |
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| A. aseg (xiao) | A. aseg (xiao) |
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| || 2 || ? || ? || || 3 || ? || ? || |
|| 2 || 100% || done || || 3 || 100% || done || |
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| B. recon-all improvements (doug) | B. recon-all improvements (doug) |
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| || 1 coding || 90 || 12/15/05 || || 2 debugging || 40 || 12/16/05 || || 3 testing || 0 || 1/3/05 || |
|| 1 || 100% || done || || 2 || 100% || done || |
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| C. miscellaneous (doug) | C. miscellaneous (doug) |
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| || 1 || 100 || done || || 2 || ? || ? || || 3 || ? || ? || || 4 || ? || ? || || 5 || ? || ? || || 6 || ? || ? || || 7 || 100 || done || |
|| 1 || 100% || done || || 2 || 100% || done || || 3 || 50% || ? || || 4 || 90% || ? || || 5 || 100% || done || || 6 || 90% || ? || || 7 || 100% || done || |
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| D. talairach failure detection, incorporated into recon-all (nick, laurence, doug) | D. talairach failure detection, incorporated into recon-all (nick, laurence, doug) |
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| E. automated testing of nightly build (kevin, nick) | E. automated testing of nightly build (kevin, nick) |
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| 3. aseg tests (xiao) | || Item # || % complete || Expected date of completion || || 1 || 90% || ? || || 2 || 90% || ? || F. verifying talairach coordinates (see VerifyTalCoords), when tal xform is known good, of: (nick, david) 1. individual surfaces and volumes 2. average surfaces and volumes |
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| || 2 || ? || ? || || 3 || ? || ? || |
|| 2 || 10% || ? || G. fix manual labelling (ev) done. |
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| F. verifying talairach coordinates, when tal xform is known good, of: (nick, david) a. individual surfaces. b. individual volumes. c. average surfaces. d. average volumes. |
H. documentation, see WikiUpdates (jenni, et al.) done. |
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| G. fix manual labelling (ev) == Work Item Notes == '''F''' (verifying talairach coordinates) The problem being addressed in this work is that the talairach coordinates supplied by Freesurfer (in tkmedit and elsewhere) are based on the alignment to the MNI305 brain, which is somewhat poorly aligned to the Talairach brain (see http://www.nil.wustl.edu/labs/kevin/man/answers/mnispace.html). The root of the problem is that the Talairach brain was never MRI scanned, and furthermore was labelled post-mordem, so it is very difficult to map a scanned brain to true Talairach coordinates. Yet we would like some assurance that the tal coordinates that Freesurfer supplies are reasonably accurate. |
I. average subject: 1. average subject area calculation (doug) 2. fix make_average_subject (doug) 3. create new average subject to replace average7 (jenni?) 4. multiple comparisons (doug) || Item # || % complete || Expected date of completion || || 1 || 100% || done || || 2 || 100% || done || || 3 || 50% || ? || || 4 || 20% || ? || |
January 2006 FreeSurfer Release
Countdown
Feb 1 was 8 days ago. 
Goals
- Post new 'stable' release, containing reliable auto-segmentation functionality, and bug fixes
- Basic automated testing of nightly-build 'dev' code base
- Updated documentation (wiki)
Work Items
A. aseg (xiao)
- make aseg work for data originating from different pulse sequences or manufactuers than the training data used to build the atlas. currently, the subcortical atlas is built from Siemens scans, and the aseg results will be quite poor if the input data is from a GE scanner. we have sw that can improve this situation a lot, but it's not very stable, and this cross-sequence option will make the aseg on Siemens data worse.
- testing to optimize the default parameters for the subcortical segmentation.
- testing of a new subcortical atlas (asegs should be better than the current atlas).
Item #
% complete
Expected date of completion
1
100%
done
2
100%
done
3
100%
done
B. recon-all improvements (doug)
- linear pipeline: in recon-all, re-naming of stuff so that files don't get overwritten later in the stream.
- test accuracy of aseg and aparc w/ mri_pretess.
Item #
% complete
Expected date of completion
1
100%
done
2
100%
done
C. miscellaneous (doug)
- total intercranial volume, using randy's method to align to talairach with skull.
- fixing tkmedit so that it implements -overlay-reg-identity properly.
- mri_surf2surf - mapping across hemispheres.
- mri_glmfit (new version of mris_glm) - mostly just need to document.
- mris_preproc - surface-based preprocessor script for mri_glmfit (does not exist but not hard).
- correction for multiple comparisons (mri_mcsim and mri_surfcluster).
- improve editing of wm with aseg
Item #
% complete
Expected date of completion
1
100%
done
2
100%
done
3
50%
?
4
90%
?
5
100%
done
6
90%
?
7
100%
done
D. talairach failure detection, incorporated into recon-all (nick, laurence, doug)
- create Matlab-compiled binary and test in recon-all stream.
- code in C and test in recon-all stream.
Item #
% complete
Expected date of completion
1
20%
postponed till after release
2
?
?
E. automated testing of nightly build (kevin, nick)
- basic tests of recon'd bert data
- tests of buckner 40+5
Item #
% complete
Expected date of completion
1
90%
?
2
90%
?
F. verifying talairach coordinates (see VerifyTalCoords), when tal xform is known good, of: (nick, david)
- individual surfaces and volumes
- average surfaces and volumes
Item #
% complete
Expected date of completion
1
70%
?
2
10%
?
G. fix manual labelling (ev) done.
H. documentation, see WikiUpdates (jenni, et al.) done.
I. average subject:
- average subject area calculation (doug)
- fix make_average_subject (doug)
- create new average subject to replace average7 (jenni?)
- multiple comparisons (doug)
Item #
% complete
Expected date of completion
1
100%
done
2
100%
done
3
50%
?
4
20%
?