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demianw / tract_querier

Implementation of the White Matter Query Language and associated tools for dMRI white matter tract extraction and analysis
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Visualisation of output tracts in TrackVis #17

Closed demianw closed 7 years ago

demianw commented 9 years ago

Called to attention by @lpetit:

Tracts that result from queries might be off-center on the visualization with TrackVis while the original tractography before the queries is well-centered:

lpetit commented 9 years ago

Hi Demian,

Does it mean that the original tractography (before tract_querier) is not in RAS while it is well-centered? How trat_querier could save a .trk using the original well-centered info?

Laurent

Laurent PETIT

GROUPE D'IMAGERIE http://www.gin.cnrs.fr NEUROFONCTIONNELLE http://www.gin.cnrs.fr UMR5296 - CNRS - CEA - UNIV. BORDEAUX

see my publications here http://www.researchgate.net/profile/Laurent_Petit3/publications/?ev=prf_pubs_p1

Université de Bordeaux, PAC Carreire 146, rue Léo Saignat, CS 61292 33076 Bordeaux Cedex

Mobile : +33 (0)671281912 E-mail : lpetit8@gmail.com

2015-02-10 8:30 GMT+01:00 Demian Wassermann notifications@github.com:

Called to attention by @lpetit https://github.com/lpetit:

Tracts that result from queries might be off-center on the visualization with TrackVis while the original tractography before the queries is well-centered:

  • This is a visualisation issue only
  • It seems to be a problem when tracts are space-encoded in a way other than RAS

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/17.

demianw commented 9 years ago

The ones you sent me are in LPI. The encoding of the coordinate system is independent of it being well centered.

Also, when I'm writing about "centered", it's always with respect to the visualisation in trackvis. What i have observed is that the volume and the tracts are always coordinated, just off the rotation center of the interface.

So any post-processing tool for stats or information extraction, such as my tract_math tool, included in the package, should output the good numbers.

Demian

lpetit commented 9 years ago

Ok! This is clear. Thanks for your help.

Laurent PETIT

GROUPE D'IMAGERIE http://www.gin.cnrs.fr NEUROFONCTIONNELLE http://www.gin.cnrs.fr UMR5296 - CNRS - CEA - UNIV. BORDEAUX

see my publications here http://www.researchgate.net/profile/Laurent_Petit3/publications/?ev=prf_pubs_p1

Université de Bordeaux, PAC Carreire 146, rue Léo Saignat, CS 61292 33076 Bordeaux Cedex

Mobile : +33 (0)671281912 E-mail : lpetit8@gmail.com

2015-02-10 10:38 GMT+01:00 Demian Wassermann notifications@github.com:

The ones you sent me are in LPI. The encoding of the coordinate system is independent of it being well centered.

Also, when I'm writing about "centered", it's always with respect to the visualisation in trackvis. What i have observed is that the volume and the tracts are always coordinated, just off the rotation center of the interface.

So any post-processing tool for stats or information extraction, such as my tract_math tool, included in the package, should output the good numbers.

Demian

— Reply to this email directly or view it on GitHub https://github.com/demianw/tract_querier/issues/17#issuecomment-73670201 .