FLIP: Autoscoper parse tiff and export .tra - inverted to stl

[amymmorton]

Required documentation:

• As part of answering TIFF & STL do not seem to align #129 , looking more thoroughly through data sets : The rigid body surface model file : stl (or .vmrl) and their associated tiff volumes are oriented [ 0 0 pi] from one another.. 'flipped'. Not only are the tiffs parsed this way- most importantly- the .tra outputs from autoscoper are exported in this 'flipped' manner. To compensate- users have created transformed bone models form original dicom orientation

• The tiff stacks do not contain metadata . Resolution and boolean if cropped (and what if so, by what tform) are necessary but currently there is no standard.