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← Revision 63 as of 2006-02-09 17:08:24 → ⇥
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Editor: NickSchmansky
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)
Line 10: Line 16:
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)
  * working to 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. '''Estimated date of completion: '''
  * testing to optimize the default parameters for the subcortical segmentation. '''Estimated date of completion: '''
  * testing of a new subcortical atlas (asegs should be better than the current atlas). '''Estimated date of completion: '''		 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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 * recon-all improvements (doug)
  * linear pipeline: in recon-all, re-naming of stuff so that files don't get overwritten later in the stream. '''Estimated date of completion: '''
  * test accuracy of aseg and aparc w/ mri_pretess. '''Estimated date of completion: '''		 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 ||
Line 20: Line 49:
 * miscellaneous (doug)
  * total intercranial volume, using randy's method to align to talairach with skull. '''Estimated date of completion: '''
  * fixing tkmedit so that it implements -overlay-reg-identity properly. '''Estimated date of completion: '''
  * mri_surf2surf - mapping across hemispheres. '''Estimated date of completion: '''
  * mri_glmfit (new version of mris_glm) - mostly just need to document. '''Estimated date of completion: '''
  * mris_preproc - surface-based preprocessor script for mri_glmfit (does not exist but not hard). '''Estimated date of completion: '''
  * correction for multiple comparisons (mri_mcsim and mri_surfcluster). '''Estimated date of completion: '''		 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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 * talairach failure detection, incorporated into recon-all (nick, laurence, doug)
  * create Matlab-compiled binary and test in recon-all stream. '''Estimated date of completion: '''
  * code in C and test in recon-all stream. '''Estimated date of completion: '''		 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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 * automated testing of nightly build (kevin, nick) 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: (nick, 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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 * improve editing of wm with aseg (?)

 * fix manual labelling (ev)		 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)

  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

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

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

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

    ?

    ?

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%

    ?

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.

H. documentation, see WikiUpdates (jenni, et al.) done.

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%

    ?

JanuaryRelease (last edited 2008-04-29 11:45:40 by localhost)