Editing Scanco Administration (section)

===Convert RSQ to PSQ===
First, in the terminal turn on the 'advanced questions' mode
<pre>
$ define uct_reconstruction_calibration true
</pre>
Second use the reconstruction EXE to convert RSQ to PSQ
<pre>
$ run UCT_RECONSTRUCTION.EXE
raw file: DISK3:[MICROCT.PROJECTS.YVES.LANDMARK.RAW]filename.RSQ

Give slice number, or 'a' for all
hit return a few times

Write Projection [N]:   -> say y and it writes the PSQ and continues with reco
Say p if it shall just produce PSQ and NOT continue with reco!
</pre>
Beam hardening correction can be turned off by doing
<pre>
$ DEFINE UCT_RECONSTRUCTION_CALIBRATION TRUE
$ define uct_disable_bh_correction true
$ deass UCT_BEAMHARD_POWER
$ deass UCT_BEAMHARD_factor
</pre>
and then run <code>uct_reconstruction</code>

The RSQ contains the RAW projection data. The PSQ represents tilted parallel beam projections:

[[Image:CB-Rebinned.gif]]

The rebinning process reduces the number of projections from 836 (1 bright field, 1 dark field and 834 projections spaced at 0.24 deg/proj, spanning 200.16 deg) to 750 (spanning 180 deg) with a resolution of 0.24 deg. In addition to the geometric changes, intensities are adjusted ln(I/I0) and beam hardening correction is applied. After converting a PSQ to AIM with IPL, an image can be reconstructed with Matlab's iradon(), note that only the central slice will be geometrically 'correct', but differences in other slices are small (Circumference of calibration phantom differs less than 1%). in the final reconstruction these effects are accounted for reducing the number of z-slices from 124 (acquired) to 110 in the reconstructed image.


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