Editing Scanco User Instructions (section)

=Evaluation=
==Evaluate a Scan==
*To evaluate a scan, refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.


===Open default ISQ===
You can load a default ISQ usig <code>uct_evaluation</code> program:

<pre>
$ def uct_default_isq DISK3:[MICROCT.PROJECTS.VALIDATION.MODELS]C0000123.ISQ   ! or
$ def uct_default_isq DISK2:[MICROCT.DATA.00001234.00005678]C0003456.ISQ
$ uct_evaluation    
</pre>

Hit <code>cancel</code> when asked files to load, and the file you just set as default will be loaded.

*Use the whole pathname for ISQ.
*If you don't import your data into the system, you cannot store your evaluation results in the measurement database.  You will have to use the LOG file to access your results.
*Only start a 3D evaluation if and only if the sample (patient) and measurement index are <b>correct</b> in the ISQ full path!  Also, no results will be stored in the database unless the ISQ header info (samp/meas) is correct.
*Many of the UCT_xxx.COM scripts use the whole filename to extract the sample and measurement numbers, so it is possible that some evaluations will not run.  UCT_xxx_BATCH_V4.COM is an example of an evaluation that will not run, but UCT_CUTOUT.COM will run (doesn't need any sample/meas info).
*A better option to execute a script is to run a <code>HIJACK</code> script as it'll ensure the sample/measurement number is captured so the results can be written to the database.


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===Errors in database writing===
Sometimes you'll find LOG files that look like this:

 EVAL_UPAT_XT2_00000000_00000000.LOG

It means that the analysis script couldn't find the sample/measurement number. This can happen for two main reasons:

:1.  If you set the <code>UCT_DEFAULT_ISQ</code> logical then the sample/measurement number isn't known. The analysis script may run, but the results won't be saved to the database.
:2. If you use the <code>UCT_EVALUATION</code> and you do the following: You go to FILE --> SELECT MEASUREMENT ... If you then hit Cancel then you still see the first scan but the patient and measurement number is set to 0/0/ on the top.

If the <code>UCT_BACKUP</code> program does not know where the IMA data is, but you know it is on the disk, you can set it's location as follows:
:* <code>SHIFT-CLICK</code> on the radio button beside the IMA field.
:* Type into the field <code>DK0</code> and it will auto-populate with a proposed path. Edit it if you need to.
:* Save the new path location

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==Draw Contours==
*Contours, or GOBJ files, are drawn to define regions of interest.  Depending on the analysis required, contours may be drawn to isolate the object from the sample tube or to separate bone compartments (e.g., cortical versus trabecular).  
*Contouring is the first step in the analysis process, which allows you to segment the desired bone from surrounding tissues.


===Contouring Tools Reference Sheet===
*[[Media:Contouring-tools.pdf |'''Contouring Tools Reference Sheet''']]
*Contours must always be drawn COUNTER-CLOCKWISE!!!  


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===Contour and Run the Standard Patient Evaluation===
The following instructions are for contouring standard patient radius and tibias. 

#Open the Evaluation Program and select your sample.
#*Refer to [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']] for general instructions on how to open the evaluation program and draw a contour.
#Zoom into the desired bone (Radius or Tibia)
#*Using the zoom menu from the top panel, zoom into the Radius or Tibia. 
#*Usually 3x zoom is appropriate.
#Draw contours roughly around the bone.
#*Select the first contouring tool (top left button) and draw COUNTER-CLOCKWISE.
#Automatically generate contours for all slices in the scan.
#*Double click the image to bring up the contouring window. 
#*Double click again and the program will attempt to snap the contour to the bone. Double click again if needed.
#*Select Forwards, and then Iterate Forwards to have the evaluation program automatically segment the bone. 
#Modify any contours as needed.
#*Select the second contouring tool (2nd button from top) to fix any "wrong" contours. 
#*Draw COUNTER-CLOCKWISE!!
#*If many contours cannot be automatically generated correctly i.e. cortical bone is porous and evaluation program misses a lot of bone, it may be better to use the Range/Morph function rather than fixing each individual slice. 
##This is done by first clearing all the breakpoints (Clear all BP in contouring window). The boxes will now become red.
##Manually fix the slice that does not have the correct contour automatically drawn, skip a few slices and manually fix that slice as well. The slices that you have fixed will turn green, indicating that it is a breakpoint (BP). 
##Now you can morph between the two breakpoints (BP, green boxes) you have just created. Select the BP with the higher slice number, select range (first column on left) from the contouring window, followed by morph (second column from left).
#Save Contour (.GOBJ): Make sure you save your work!
#Run the 3D Standard Evaluation for your specific project (and timepoint). 
#*Select 3D evaluation under Tasks to bring up the window. You'll then need to Select... the evaluation specific for your project. 
#*There are a variety of evaluations to choose from, you can search for your project's evaluation script by typing in the name of your project in the filter window. 
#Check the queue to ensure that the evaluation is running properly.
#*Type <code>$ show que</code> in a terminal window will allow you to see all running processes.


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===Correct Trabecular Contours and Run the Cortical Evaluation===
Once the standard evaluation has been completed, an auto-segmentation process is completed to segment the cortical from the trabecular bone. However, the auto-segmentation is not always accurate, and hence the contour (TRAB.GOBJ) will need to be checked.

#Load TRAB.GOBJ by selecting File, then load GOBJ from the top panel.
#*You will now see a list of all GOBJ files pertaining to your sample. You'll need to load the TRAB.GOBJ.
#*When the TRAB.GOBJ has loaded, you will see that the loaded contour is between the cortical and trabecular bone.
#Correct contours as needed
#*Can manually adjust the slices or use the Range/Morph function. 
#*Remember to draw COUNTER-CLOCKWISE!
#Run the 3D cortical evaluation for your specific project (and timepoint, if relevant). 
#*Select 3D evaluation under Tasks to select the appropriate evaluation script. 


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==Evaluation Scripts==
===Scanco Standard Evaluation Scripts===
The following are descriptions of some of the standard evaluation scripts provided by Scanco Medical.  

*'''3D Segmentation of VOI, 1 solid object'''
:Produces a 3D segmented (binary) object with values 0 (background, hidden) and 127 (solid).  Input Gaussian filtering and threshold parameters.  Draw contour to isolate the object of interest (optional).

*'''3D Seg. of 2 VOIs: solid dense in transparent low dens obj'''
:Produces a 3D segmented object with values -1 (transparent), 0 (background, hidden), and 127 (solid). Input two sets of Gaussian filtering and threshold parameters (input the second set by pressing the red 2 button).  The preview shows the solid object in white and the transparent object in red.  Draw one contour to isolate the object of interest (optional).  This script is useful for showing soft tissue and bone.

*'''Bone Trab. Morphometry (3D Seg, 3D Calc, Print Sheet)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour to isolate the trabecular bone.  Performs model-independent (direct) measurements on the trabecular region.  Outputs:  BV, TV, BV/TV, TbBMD, TbTMD, BS, SMI, DA, ConnD, TbTh, TbThSD, TbSp, TbSpSD, TbN, and Tb1/NSD.

*'''BV/Density only Bone Eval. (3D Seg, BV and Dens Calc, Print)'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour to isolate the region of interest.  Outputs:  BV, TV, BV/TV, BMD, and TMD.

*'''Bone Midshaft Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour on the outer surface of the bone.  Outputs:  BV, TV, BV/TV, BMD, TMD, and moment of inertia parameters.

*'''Bone Midshaft more than e.g. 50 slices Evaluation'''
:Produces a 3D segmented object with values 0 (background, hidden) and 127 (solid) from Gaussian filtering and threshold inputs.   Draw contour on the outer surface of the bone.  If you wish to exclude the medullary area from the analysis, then draw a counterclockwise contour on the outer surface of the bone and a clockwise contour on the inner surface of the bone.  Performs direct measurements in addition to the standard midshaft analysis.  Outputs:  BV, TV, BV/TV, BMD, TMD, moment of inertia parameters, Th, and Sp.

*'''Convert to TIFF'''
:Converts the grayscale data to TIFF slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Convert to DICOM'''
:Converts the grayscale data to DICOM slices for the region inside the white evaluation box. The converted files are output into the scan directory.

*'''Reformat to Axial Cuts'''
:Flips the dataset from the XY plane to the XZ or YZ planes (specify in the advanced options for the script). This is useful if you want to contour your sample in a different plane.  The flipped sample is imported as a new measurement under the same sample number as the original data.


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===Understanding Evaluation Scripts===
Following are some example evaluation scripts full of comments to promote understanding:
*[[Media:IPLV6_VOI.pdf|IPLV6_VOI script]]
*[[Media:IPLV6_MIDSHAFT.pdf|IPLV6_MIDSHAFT script]]
*[[Media:IPLV6_TRABECULAR_BONE.pdf|IPLV6_TRABECULAR_BONE script]]


===Setup Customized Evaluation Scripts===
To setup an evaluation script customized to your project, in the [[Scanco_User_Instructions#.C2.B5CT_Evaluation_Program|'''µCT Evaluation Program''']]:
*Choose "Scripts" then "Import from" then "TEMPLATES", pick a Scanco Standard Evaluation Scripts and Save.  
*Choose "Scripts" then "Modify".  Choose the script that was just imported and click "OK",  Change the name of the script.  
*Modify the default segmentation and other parameters for the script.  When finished making changes press "Save" then "OK".


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==Image Processing Language (IPL) Scripting==
The following documentations related to IPL scripting, as it applies to image analysis was compiled by Jan Owoc in July 2013 based on numerous sources including own experience.

===Your First IPL Script===
*'''Prerequisite''': you are familiar with navigating the VMS system. 
*'''"$" or "ipl>"''': the DCL and IPL prompts respectively, and you should only type the text after the prompt. 
*If you FTP the file to the OpenVMS system, ensure you use "binary" to transfer the file.
You can run these commands on almost any greyscale AIM file. Example file here: MJ7101.AIM 


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====Interactive IPL====
*Command <code>$ ipl</code> starts IPL interactively, that is you see the result of each command as you run it. 
*While it is useful for testing, running large scripts interactively may interfere with others using the computer. 
<br>
*'''Reading an AIM file'''
:Before you can run any analysis on the AIM file, you need to read it into IPL and assign it a file handle. This is done using the command <pre>ipl> read in MJ7101.AIM</pre>
:A fraction of a second later, the file should have been read into memory and assigned the internal name "in". If we want to do some basic density calculations on it, we can use the command<pre>ipl> vox_ in 0</pre>
:*IPL, much like DCL, will automatically complete the command if it is given enough characters. 
:The "vox_" was expanded to the command "vox_scanco_param" (calculates voxel-counting parameters) and told you that the mean density of the cube is 114 mg HA/cm3 and a standard deviation of 283 mg HA/cm3. 
:The argument "in" is the internal name of the image.
:The argument "0" is the region. The command vox_scanco_param supports several numbered regions if, for example, you wanted to separately compute the density for the trabecular region and the cortical region.
<br>
*'''Segmenting an AIM file'''
:Some parameters, like average density, are computed from the [[Scanco_User_Instructions#Grayscale_Images|'''Greyscale Image''']]. Other parameters, like the trabecular number, require an image that has been segmented to [[Scanco_User_Instructions#Binary_Images|'''Binary Images''']], that is converted into "bone" and "not bone". 
:There are many ways to separate bone from non-bone, and parameters that work well for one dataset will not generally work for images of different samples, or acquired at different resolutions.
:One of the simplest segmentation methods "seg_gauss" is to apply Gaussian smoothing to the sample, to eliminate the noise present in the image, followed by a semi-arbitrary threshold that preserves the trabecular structure. 
<pre>
ipl> seg_gauss in seg

  -sigma                     [1.000000] >  
  -support                   [2] > 
  -lower_in_perm_aut_al      [300.000000] > 
  -upper_in_perm_aut_al      [100000.000000] > 
  -value_in_range            [127] > 
  -unit                      [0] > 2 
</pre>
:seg_gauss expects 8 parameters, and we have provided only 2. It will now prompt us for the remaining 6 one-by-one. 
:Leave everything at the defaults (simply hit "Enter") except the unit, which we will change to "2". 
:For young human trabecular bone from the distal tibia scanned at 20 um in the uCT 35, but then downscaled to 80 um, the above parameters give a reasonable representation of the trabecular structure. With other bones at other resolution, you may need to change the sigma, the support, and the lower threshold. 
:The unit of "2" simply means that we are working in units of mg HA/cm3.
:Now that the cube is segmented, we can run the same voxel-counting command as above and obtain more information. <pre>ipl> vox_ seg 0</pre>
:We now know that our combination of smoothing and threshold resulted in an object volume of 103 mm3 (i.e. volume of bone) and a bone volume ratio of 22.88%.
<br>
*'''Writing out a file'''
:we can write the segmented file out for future use. Accept the defaults for the remaining arguments. <pre>ipl> write seg MJ7101_SEG.AIM</pre>
:Now you can quit IPL and verify that the segmented file has been written out. <pre>ipl> quit</pre>


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====Batch IPL====
*Command <code>$ ipl_batch</code> starts IPL inside a script that would be submitted to a queue.
While the following code is likely to work, it is not very readable:
<pre>
$ IPL_BATCH
read in MJ7101.AIM
vox_ in
seg_gauss in seg 1 2 300 100000 127 2
vox_ seg
write seg MJ7101_SEG.AIM
..
$ EXIT
</pre>
*Instead, it is recommended that you copy and paste the "pretty" output of the command after you have run it once interactively.
*Values that are likely to change should be variables, defined at the top of the script. 
*To substitute a variable from DCL into IPL, use a double-quote character before the variable name, as shown in the example below. 
Copy and paste the below into a text editor.
<pre>
$ modelname  :== MJ7101.AIM
$ threshold   == 300
$ outputfile :== MJ7101_SEG.AIM
$
$ IPL_BATCH

/read
  -name                      in
  -filename                  "modelname

/vox_scanco_param
  -input                     in

/seg_gauss
  -input                     in
  -output                    seg
  -sigma                     1.000000
  -support                   2
  -lower_in_perm_aut_al      "threshold
  -value_in_range            127
  -unit                      2

/vox_scanco_param
  -input                     seg

/write
  -name                      seg
  -filename                  "outputfile 

..
$ EXIT
</pre>
Now, it is clear what the full names of the commands are, and what the parameters mean. 
*If a parameter isn't important and can be left at the default (for example the region number during vox_scanco_param), you can leave it out of the file. 
Save the file as MYSCRIPT.COM and run it using <code>@MYSCRIPT.COM</code>.

<br>
*'''Submitting to the queue'''
:As mentioned in the introduction, running IPL interactively on larger models negatively impacts other users of the system. Copying the commands to a file and running it from the command line has the same effect. 
:*The correct way to run larger scripts is to submit the job to the queue. <pre>SUBMIT/QUE=SYS$FAST MYSCRIPT.COM</pre>


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===IPL Reference===
*[[Media:SCANCO_-_Software_-_IPL_instruction_manual_0.pdf|'''Official Scanco IPL Documentation''']] 
*[[Media:scanco-software-ipl-instruction-manual.pdf|'''Scanco IPL Manual]]


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====Standard Read Write etc. Functions====
*'''/read''': Reads a file into ipl and gives the file an internal name 
*'''/aim_read''': 
*'''/read_versatile''': 
*'''/write_v020''': Writes an aim file to the directory in which ipl is open (or specified directory if in a script)
*'''/write_new''': 
*'''/write_part''': 
*'''/copy''':  Copies an internal file (a file that is already in the ipl system) and allows the copy to be given a new name.
*'''/delete''':   Deletes an internal file (a file that is already in the ipl system)
*'''/rename''':  Changes the name of the file (input is the old name and output the new name)
*'''/list''': 
*'''/options''': 
*'''/release_history''': 
*'''/commands_write_log''': 


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====Segmentation Functions====
*'''/gauss_lp''': Applies a low pass gaussian filter with specified sigma and support values
*'''/fft_laplace_hamming''': 
*'''/median_filter''': Applies a low pass median filter to reduce unwanted noise in an image
*'''/seg_gauss''': Segments aim files using the input sigma of gauss and the filter support for gauss.  A threshold can also be applied using this function.
*'''/threshold''': Removes data outside of the specified range 
*'''/absolute_threshold''': 
*'''/adaptive_threshold''': 
*'''/adaptive_iter_threshold''': 
*'''/matching_threshold''': 


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====Gobj and Masking Functions====
*'''/gobj_maskaimpeel_ow''': Cuts an aim file with a gobj so that only the portion of the aim within the gobj remains. Peel_iter value used to specify the number of pixels within the gobj the function will need to cut.
*'''/gobj_to_aim''': Reads a gobj file from the directory and makes an aim file (the aim file is in ipl, to output it to the directory use write).
*'''/togobj_from_aim''': Takes an aim file and writes a gobj file (the gobj is output to directory).  
*'''/gobj_circumf_area''': 
*'''/gobj_join''': 
*'''/gobj_join_consec''': 
*'''/gobj_scale''': 
*'''/gobj_isotrop''': 
*'''/cortex_maskoff''': 
*'''/peel3d''': 

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====Voxel-Counting, Density and Triangulation Functions====
*'''/db_scanco_activate''': 
*'''/db_clear_eval''': 
*'''/db_calib_unit_fill''': 
*'''/db_set_mean_accur''': 
*'''/voxgobj_scanco_param''': Inputs an aim file and a gobj and provides information (including total volume, object volume and the mean value of the points)  on the region within the gobj.  
*'''/vox_scanco_param''': Inputs an aim and provides information including total volume, object volume and the mean value of the points. 
*'''/tri_da_metric_db''': 
*'''/tri_direc_distr''': 
*'''/connectivity''': Receives a component labelled aim object and calculates the connectivity of the labelled components.
*'''/conn_nocl''': 
*'''/conn_bgcl''': 
*'''/fractal_dimension''': 

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====Distance Transformation (Sphere Filling) Functions====
*'''/dt_object_param''': 
*'''/dt_ow_object_param''': 
*'''/dt_background_param''': 
*'''/dt_mat_param''': 
*'''/dt_cortex_obj_param''': 
*'''/dt_value_output''': 
*'''/dt_mat_output''': 

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====Statistical Functions====
*'''/examine''': Receives an AIM object and outputs specified information based on the item input.
*'''/histo''': 
*'''/moment2d_of_inertia''': 
*'''/moment3d_of_inertia''': 
*'''/zmeanmax''': 

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====Voxelsize-Scaling Functions====
*'''/isotrop''': 
*'''/scale_elsize''': 
*'''/ipscale_elsize''': 
*'''/noipscale_elsize''': 
*'''/scale_ow_elsize_noip''': 

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====Component Labeling Functions====
*'''/cl_ow_rank_extract''': Receives AIM file and over writes it with an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl_rank_extract''': Receives AIM file and outputs an AIM containing the extracted and component labelled pieces based on their size. First_rank specifies the largest selected piece to be extracted and last_rank specifies the last selected piece.
*'''/cl26_rank_extract''': 
*'''/cl_image''': 
*'''/cl_extract''': 
*'''/cl_slicewise_extractow''': 
*'''/cl_nr_extract''': 

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====Add, Concat, Cut etc. Functions====
*'''/add_aims''': Adds the values of two AIM images in a 3D space.
*'''/add_constant_ow''': 
*'''/border_change''': 
*'''/bounding_box_cut''': Cuts extra space out of an aim file so that only the region with the data remains. A border can be added to the image using the border input.
*'''/concat''': Takes two aim files and combines them.  The data from both aims or just the common region can be kept.  To add the images add_not_overlay is set to true (for example if image 1 has a value of 41 and image 2 has a value of 82, the combined value will be 123).
*'''/concat_adapt''': 
*'''/divide_volumes''': 
*'''/fill_min_max_ow''': 
*'''/header_geo_set''': 
*'''/header_log_set''': 
*'''/header_calib_ov''': 
*'''/invert_ow''': 
*'''/mult_constant_ow''': 
*'''/multiply_volumes''': 
*'''/sqr_to_float''': 
*'''/sqrt_to_float''': 
*'''/offset_add''': 
*'''/offset_set''': 
*'''/clear_offset''': 
*'''/fill_offset_mirror''': 
*'''/fill_offset_duplicate''': 
*'''/set_value''': Sets the values of the object and background of an aim file to chosen values
*'''/sub_get''': Extract a portion of an image <br />
**-pos corresponds to x,y,z origin -1 -1 -1 maintains the original coordinates <br />
**-dim corresponds to x,y,z dimensions -1 -1 -1 maintains the original dimensions (within maximum range) <br />
**indexing starts at 0 instead of 1
*'''/sub_pick''': 
*'''/subtract_aims''': Subtracts one aim from another and outputs the remaining region. 
*'''/sup_divide''': 
*'''/transparent_concat''': 

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====Erosion Dilation Open Close Functions====
*'''/erosion''': 
*'''/dilation''': 
*'''/open''': 
*'''/close''': 
*'''/erosion_dilat_variable''': 

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====Import Export Conversion Norming Functions====
*'''/import_freeformat''': 
*'''/dicom_to_aim''': 
*'''/todicom_from_aim''': 
*'''/dicom_list_series''': 
*'''/isq_to_aim''': 
*'''/isq_gobjfit_to_aim''': 
*'''/toisq_from_aim''': Writes an isq file to the directory ipl is open in (or specified directory) from an aim file.  The isq name should be 8 characters long.  
*'''/mesh''': 
*'''/msq_from_aim''': 
*'''/rsq_to_aim''': 
*'''/stl_tri''': 
*'''/convert_to_type''': 
*'''/convert_unsigned''': 
*'''/norm_max''': 

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====Functions for Root Canal Evaluations====
*'''/separ_roots''': 
*'''/calc_ctr_mass_list''': 
*'''/calc_ctr_mass_diff''': 
*'''/treated_surf''': 
*'''/match_cut''': 
*'''/match_cut_adapt''': 

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====Miscellaneous Functions====
*'''/align_z''': 
*'''/dcl''': 
*'''/flip_aim''': 
*'''/growback_to_orig''': 
*'''/turn3d''': 
*'''/turn2d''': 
*'''/upat_filldb''': Fill special Upat DB for patient (radius/tibia) evaluation
*'''/xray''': 

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====Obsolete, Experimental and Duplicate Functions====
*'''/curv_tri''': 
*'''/cut2D_shape_ow''': 
*'''/join_uncompress''': 
*'''/mil_param''': 
*'''/milv1_param''': 
*'''/gauss_seg''': duplicate of /seg_gauss
*'''/from_aim_to_isq''': The function toisq_from_aim will also convert an aim to an isq 
*'''/local_threshold''': 
*'''/edge_canny''': 
*'''/sobel_grad''': 
*'''/hysteresis_thresholg''': 

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====Functions only available in iplfe====
*'''/register''': Registers two aim files and output a transformation matrix of the transformation to moving input 2 into the space of input  1. Gobjs can be input (registration is more successful with gobjs).  Orientation search can be done with masscenter, and/or moment of inertia (MoI), or degree intervals. 
*'''/transform''': Transforms an aim file using a transformation matrix (a text file of the matrix can be input).  Interpolation options are nearest neighbor, linear, and cubic interpolation.  The inverse of the transform provided can be done by setting Tmat_invert to true.  
*'''/fe_solveD''': A number of finite element functions are available in iplfe, not all are listed here


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