Changes between Version 12 and Version 13 of barSoftwareParsersAba


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Timestamp:
12/01/11 00:23:32 (8 years ago)
Author:
danek
Comment:

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  • barSoftwareParsersAba

    v12 v13  
    66 
    77  1. Fetch `AtlasAnnotation25.sva` sparse volume file from [http://community.brain-map.org/confluence/download/attachments/525267/data.zip?version=1 ABA Website]. 
    8   2. Coordinates in this volume are expressed in  [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAvoxel_1.0] (`ABAvoxel, INCF:0100`) SRS, in which units of measurements are voxels. In order to express coordinates in stereotaxic coordinates (with bregma point as origin of the coordinate system), the volume has to be transformed into [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAreference_1.0] SRS (`ABAreference, INCF:0101`). 
     8  2. Coordinates in this volume are expressed in  [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAvoxel_1.0] (`ABAvoxel, INCF:0100`) SRS, in which units of measurements are voxels. In order to express data in stereotaxic coordinates (with bregma point as origin of the coordinate system), the volume has to be transformed into [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=ListSRSs Mouse_ABAreference_1.0] SRS (`ABAreference, INCF:0101`). 
    99 
    1010  3. Such transformation is given by the [http://code.google.com/p/incf-dai/wiki/AtlasRequestInterfaceSpec#TransformPOI TransfomPOI] INCF DAI service (ie. [http://incf-dev.crbs.ucsd.edu/aba/atlas?service=WPS&version=1.0.0&request=Execute&Identifier=TransformPOI&DataInputs=transformationCode=Mouse_ABAvoxel_1.0_To_Mouse_ABAreference_1.0_v1.0;x=1;y=112;z=162 this request]). 
    1111 
    12   4. Tranformation may be calculated from 4 points in `ABAvoxel` SRS (`p1, p2, p3, p4`) and 4 corresponding point in `ABAreference` SRS (`p1', p2', p3', p4'`) by solving following equation: 
     12  4. Tranformation may be calculated from 4 points in `ABAvoxel` SRS (`p1, p2, p3, p4`) and 4 corresponding point in `ABAreference` SRS (`p1', p2', p3', p4'`) by solving the following equation: 
    1313 
    1414  [[Image(gif.latex.gif)]] 
    1515 
    16 After all, matrix '''M''' is: 
     16After all transformations, matrix '''M''' reads: 
    1717{{{ 
    1818 
     
    7979}}} 
    8080 
    81 Then, initial volume from `AtlasAnnotation25.sva` is transformed using '''M'''' and the resulting volume is used by the 3dBAR parser to create CAF dataset. 
     81Then, an initial volume from `AtlasAnnotation25.sva` is transformed using '''M'''' and the resulting volume is used by the 3dBAR parser to create CAF dataset. 
    8282 
    8383Below you may find comparison of brain outlines created using raw volume (dark gray) and volume after transformation (light gray): 
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