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Comment: mri_mcsim -- not needed anymore, subsumed into mri_glmfit
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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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| == Work Items Summary == | == Work Items == A. aseg (xiao) 1. 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. 2. testing to optimize the default parameters for the subcortical segmentation. 3. 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 || |
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| * aseg (xiao) | B. recon-all improvements (doug) 1. linear pipeline: in recon-all, re-naming of stuff so that files don't get overwritten later in the stream. 2. test accuracy of aseg and aparc w/ mri_pretess. || Item # || % complete || Expected date of completion || || 1 || 100% || done || || 2 || 100% || done || |
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| * improve editing of wm with aseg (?) | C. miscellaneous (doug) 1. total intercranial volume, using randy's method to align to talairach with skull. 2. fixing tkmedit so that it implements -overlay-reg-identity properly. 3. mri_surf2surf - mapping across hemispheres. 4. mri_glmfit (new version of mris_glm) - mostly just need to document. 5. mris_preproc - surface-based preprocessor script for mri_glmfit (does not exist but not hard). 6. correction for multiple comparisons (mri_surfcluster). 7. 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 || |
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| * linear pipeline, recon-all improvements (doug) | D. talairach failure detection, incorporated into recon-all (nick, laurence, doug) 1. create Matlab-compiled binary and test in recon-all stream. 2. code in C and test in recon-all stream. || Item # || % complete || Expected date of completion || || 1 || 20% || '''postponed till after release''' || || 2 || ? || ? || |
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| * test accuracy of aseg and aparc w/ mri_pretess (doug) | E. automated testing of nightly build (kevin, nick) 1. basic tests of recon'd bert data 2. tests of buckner 40+5 || Item # || % complete || Expected date of completion || || 1 || 90% || ? || || 2 || 90% || ? || |
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| * talairach failure detection, incorporated into recon-all (nick, laurence, doug) | 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 || Item # || % complete || Expected date of completion || || 1 || 70% || ? || || 2 || 10% || ? || G. fix manual labelling (ev) done. |
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| * verifying talairach coordinates, when tal xform is known good, of: (david) 1. individual surfaces. 2. individual volumes. 3. average surfaces. 4. average volumes. |
H. documentation, see WikiUpdates (jenni, et al.) done. |
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| * total intercranial volume, using randy's method to align to talairach with skull (doug) * fix manual labelling (ev) * automated testing of nightly build (kevin, nick) |
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_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%
?