Editing Scanco Administration (section)

==IPL FAQ==
===Submit a job to the queue===

<pre>
$ submit/noprint /que=sys$slow ipl_voi_josh_m.com /log=sys$scratch:test.log
</pre>


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===Rotate with turn3d / turn2d===

The turn3d function can be used to perform a single rotation about any axis in 3d.  The turnaxis_angle input is the angle between the x, y, and z axes and the line about which the rotation will be performed.  The turnangle input is the amount to be rotated about the specified line.  To use this function to perform three sequential rotations about the image's original x, y, and z axes requires compensation for the previous rotations.

To rotate an image from the axial view in the z plane to the sagittal view in the z plane: 

<pre>
$ipl
/turn3d
  -input &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;   in
  -output &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;     out
  -turnaxis_angles     90 0 90
  -turnangle           90
  -img_interpol_option        0
</pre>

No interpolation is necessary as this is "pure reformatting" (turning +-90 or 180 degrees around x,y or z axis)

For knee images, to put the femur above the tibia, you further add the step:

<pre>
/turn2d
  -input                      out
  -output                     happyFemur
  -turnangle                  270
  -turnpoint_global_not_local true
  -turnpoint                  -1 -1
  -img_interpol_option        0
 </pre>

Refer to [[Media:turn3d.pdf |'''turn3d.pdf''']] for further instructions. 


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===Noise removal by component labeling===
*Refer to [[Media:ComponentLabeling.pdf|'''Noise removal by using component labeling''']]


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===Create MSQ image and view===

This is based on marching cubes.  See <code>IPL_UPAT_EVAL.COM</code> for an example as per below:

<pre>
/read seg C0000214_SEG.AIM

/sup_divide                               ! careful of the order of inputs here
  -input                     seg
  -suppos_pixels_local       -1 -1 -1
  -supdim_numbers            1 2 1
  -subdim_pixels             -1 -1 -1
  -testoff_pixels            0 0 0

/sub_pick
  -input                     seg
  -output                    segsub
  -subpos_numbers            0 1 0

/tri
  -input                     segsub
  -output                    tri
  -gobj_filename             none
  -peel_iter                 0
  -ip_sigma                  0.8
  -ip_support                1
  -ip_threshold              40
  -nr_ave_iter               2
  -size_image                512 512
  -scale_image               0.800000
  -edges                     false
  -nr_views                  1             ! Important

/msq_from_aim
  -aim_name                  tri
  -msq_filename              C0000123_3D.MSQ
</pre>

Then, use <code>UCT_3D</code> to view it.  If you click on "animations" it will give you the option to read the MSQ file.


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===db_scanco_activate associate evaluation database===

When <code>/db_scanco_activate</code> is used in the IPL files, the correct association with the evaluation database is through the Index Patient and Index Measurement in the AIM header.

<pre>
Index Patient                                    3095
Index Measurement                                5962
!-------------------------------------------------------------------------------
</pre>

Using IPL
<pre>
$ ipl
$ read in xxx.aim
$ examine in log
$ db true           {activates database}
$ dt_object         {at end "writing results to database for measurement 1234"}
</pre>


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===dicom_to_aim bug in IPL v5.03===

In IPL, use the /dicom_to_aim function.  There is a bug in pre IPL v5.03 which requires that a small AIM be read in before doing the DCM conversion.
<pre>
ipl> read in tmp.aim
ipl> dicom_to_aim
  -aim_name                  [in] > 
  -dicom_filename            [default_file_name] > 4F65038B3986.DCM
  -multifile                 [false] > true
ipl> write in MYFILE.AIM
</pre>


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===Understand "New" DT functions in IPL v5.42===

This applies to:
<pre>/distance_map              /dt_ow_thickness           /dt_number                
/dt_thickness              /dt_spacing                /dt_cortical_thickness
</pre> 

XT1 (old dt) and XT2 (new dt) use 0.5 for assign_epsilon and 0.9 for
ridge_epsilon.

µCT uses 1.8 for assign_epsilon and 0.9 for ridge_epsilon (old dt).

Therefore I recommend to take 0.9 and 1.8 also for the new dt functions
for µCT/vivaCT measurements.

The <code>suppress_boundary</code> feature is new and works as follows:

0: The ridges and spheres are calculated on the full seg AIM, also
outside the gobj. At the end the gobj is applied.

1: The ridges that are on the AIM boundary are not used for the
calculation of the maximal spheres.

2: The ridges are calculated on the full seg aim but then the gobj is
applied to the ridges. This means that at the end there are only spheres
that have the center inside the structure (gobj). The maximal sphere
filling algorithm still accounts for the structure outside the gobj, but
only uses center points inside the gobj.


<code>dt_thickness</code> for example can be used in two different ways in a script:

1) cut out aim - apply threshold - apply gobj - dt_thickness
This way the suppress_boundary options do influence the results
because there are no ridges outside the gobj anyway.

2) cut out aim - apply threshold - dt_thickness (with corresponding gobj)
This calculates the dt on the full aim first and applies then the
gobj and suppress options.

If you examine for example trabecular bone only on a small area bounded
by a gobj then the most accurate way to calculate the dt is to cut out a
much larger area (still containing trabecular bone) and use way 2) above
with suppress_boundary 0.


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===Develop new IPL commands in C===
*Refer to [[Media:IPL programming.doc|'''A short manual on how to develop new IPL commands in C'''.]]


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