Editing Scanco Administration (section)

===Measure RSQ motion artifact===
Based on RSQ data, in-plane translation and rotation, and longitudinal translation can be determined. 

The RSQ is first converted to a tilted parallel-beam sinogram. Motion is measured using the bonelab_measuremotion command in the Calgary extension of IPL installed on percy. Copy the motion scripts available in <code>DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]</code> to your COM directory. Here is how they work:

* RSQ_TO_PSQ.COM;1 - (optional) convert RSQ to PSQ, PSQ gets created in the same directory as RSQ. Usage:

<code>$ @rsq_to_psq.com DK0:[BRUNO.DATA.00000162.00009479]C0008921.RSQ</code>

* IPL_MEASUREMOTION.COM;2 - Takes a PSQ and measures motion using Calgary IPL on percy

<pre>
$! example of how to submit a motion measurement
$ SUBMIT/NOPRINT/QUE=SYS$FAST /LOG=SYS$SCRATCH: -
  DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM -
  /PARAM=(DISK3:[MICROCT.PROJECTS.DEVEL.RECO_TEST.RAW]PHANTOM_NOMOTION.PSQ) -
   /LOG=DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]MEASUREMOTION.LOG
</pre>

Results are save in <code>MEASUREMOTION.LOG</code> and the following section contains all information:
<pre>
/bonelab_measure_motion
  -input                     org
Motion:
Translation = 2.135364
Rotation = 0.024216
Index = 3.694660
Translation weight = 0.943156
Rotation weight = 69.403737
Z_motion = 2.274551

Use the line below with search.
Translation,Rotation,Index,Trans_weight,Rot_weight,Z_motion
2.135364,0.024216,3.694660,0.943156,69.403737,2.274551

Use the line below for DB entry (Index*100).
db_motion_index=369.466034
</pre>

In-plane translation is '''Translation''', in-plane rotation is '''Rotation''' and longitudinal translation is '''Z_motion'''. '''Index''' is the total in-plane motion as used in the IEEE ISBI 2009 paper by linear combination using the weights, not used any more, now we use in-plane translation only. '''db_motion_index''' is the motion index value multiplied by 100 and that could be written to the patient database. Multiplication by 100 is necessary since the motion field in the database is integer only.

For more background on the algorithm look at ''Pauchard Y., et al, Measuring patient motion in HR-pQCT, IEEE ISBI 2009'', and ''Pauchard Y., et.al., Automated quantification of three-dimensional subject motion to monitor image quality in high-resolution peripheral quantitative computed tomography, Phys Med Biol. vol. 56, pp 6523-6543, 2011''. '''IMPORTANT''': The IPL implementation has not been validated against the Matlab implementation used in these publications. Motion Values can be different. Values can be automatically extracted as described below.

* RSQ_MEASUREMOTION.COM;10 - The full deal: creates PSQ and measures motion all in the same directory as the RSQ.
<code>
@DISK3:[MICROCT.PROJECTS.RESCAN.COM]RSQ_MEASUREMOTION.COM DISK3:[MICROCT.PROJECTS.RESCAN.RAW]M0003508.RSQ;1
</code>

Make sure to adjust the line:
<code>$ SCRIPTFILE := DISK3:[MICROCT.PROJECTS.YVES.SCRIPTS]IPL_MEASUREMOTION.COM</code>
to the location of your <code>IPL_MEASUREMOTION.COM</code>.

The results are stored in the same directory as the RSQ in <RSQname>MOTION.LOG and can be extracted into motion_all.txt by running the search command:
<pre>search/output=motion_all.txt/window(0,1)/match=OR *motion.log "Translation,","Patient Name "</pre>


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