Editing Scanco User Instructions (section)

=Results=

==Images and Animations==
Refer to [[Scanco_User_Instructions#.C2.B5CT_Ray|'''µCT Ray''']] for detailed instructions.

===[[#Change_the_View|Change View]]===
===[[#Change_the_Colours|Change Object Colors]]===
===[[#Cutplane_and_Subdim|Show a Section-View of an Object]]===

===Save a Screetshot Image===
#Open XV from a dec terminal on a workstation by typing <code>$ xv</code>. 
#Open and frame the image, program etc. that you would like to save an image of.
#In XV, click GRAB. You can either autograb the entire screen after a delay or manually grab a desired area.
#After grabbing the desired section, click Save in XV.

===[[#Save_the_Image|Save Image]]===
===[[#Save_for_Animation|Save Frames for an Animation]]===

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===Convert AIM to TIF series===

Use the utility SEQ_TO_IMAGE located in the UT directory.  A symbol has been set up to run this called TIF.

<pre>
$ mcr ut:seq_to_image
Program: seq_to_image V1.1b
Input-File []: WISDOM_L_R05.AIM
File Format [TIF]: 
Default TIF Names: WISDOM_L_R05_xxxx.TIF

Output-File [WISDOM_L_R05]: 
!> Reading AimVersion020 
Start Slice [0]: 
End Slice [179]: 5
Number of images thereof (count) [6]: 
Scale Factor (Integer) [1]: 
global_pos (1=true, 0=false) [0]: 
Max value to norm to 255 [32767]: 
Slice: 0
Slice: 1
Slice: 2
Slice: 3
Slice: 4
Slice: 5
$ dir wisdom*

Directory DISK1:[MICROCT.SCRATCH]

WISDOM_L_R05.AIM;1  WISDOM_L_R05_0000.TIF;1                 WISDOM_L_R05_0001.TIF;1
WISDOM_L_R05_0002.TIF;1                 WISDOM_L_R05_0003.TIF;1
WISDOM_L_R05_0004.TIF;1                 WISDOM_L_R05_0005.TIF;1

Total of 7 files.
$ 
</pre>


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===Generate TIF (or others) from 3D rendered volume===

This replaces uct_movie that operated on the alpha systems. UCT_3D can be called in batch mode.

A pdf describing this tool is located here: [[Media:UCT_RAY V4.0-1.pdf]] 

To interactively declare the desired settings:
<pre>
$ uct_3d_batch
?CT RAY_BATCH V4.0-1

UCT_R: Application initialized
Filename             []: 
Print-Filename       [SYS$SCRATCH:TEMP_3D.PS]: 
Ambient   (0.0..1.0) [0.200]: 
Shadows        (0/1) [1]: 
Size       (1..1024) [1024]: 
Elevation  (-90..90) [30]: 
Rotation (-180..180) [35]: 
Copies        (0..9) [1]: 

</pre>

To apply a saved set of settings, a setup-file can be created by running uct_3d in interactive mode. Select "Presets" from the toolbar and save the settings you desire (e.g. elevation 90, rotation 0).

<pre>
$ uct_3d_batch setup-file [data-file printfile]

Examples:

$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.ps
$uct_3d_batch uu:3d_preset_test.dat myaimfile.aim sys$scratch: x.tif

</pre>

You can also add/remove patient name, etc, in <code>options -> object/display properties</code>. Make sure you render your image before you save your preset!

To automatically generate tifs for many files, a script was created to replace PRINT_3D.COM
The script is currently stored in the xtremect2 com directory.

<pre>
@COM:PRINT_REG_TIF.COM

 Generates a 3D image from a segmented file.  

 The outputs include:
  - two 3D renderings (TIF)

 Use full pathnames for the segmented AIM.

 P1 - Segmented AIM

 Usage:
 @COM:PRINT_REG_TIF.COM DISK2:[MICROCT.DATA.00000379.00001376]C0001234_SEG.AIM
</pre>

This script can be modified to  use a custom preset file.


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===Make an Animation===

To calculate an Animation, two (separate) tools of the 3D program are used: the set-up of start and end point of the Animation, and the 'Auto-Print' tool that automatically creates the TIF files for every rendered image.

This is a 'step by step' guide to create an animation using TIFF files:
:* Open your sample in the 3D program.
:* Now, open 'options','Animation'
:* Render your Image the way you want your animation to start. e.g. observer rotation -179 degrees. You may interrupt if you want. If you are satisfied with all the settings (rotation, elevation, transparency, colors etc.) the Click on 'Get Settings A'
:* Then, adjust all the settings for the endpoint of your animation (with the mouse or the sliders) e.g. observer rotation +179, and start the rendering. If satisfied, click 'Get settings B' 

<b>Note:</b> To test, put # of views to 5 or 10... You can also interrupt the build-ups for faster viewing.
:* Click the START button again, wait till the build-up of the 3D image is finished.
:* DO NOT HIT 'START CALCULATION' YET!
:* First, you also need to set-up the 'Auto-Print' mode:
:* Go to the 'Print' menu (file --> print), choose print to TIF and to File and enter THE BEGINNING OF A FILENAME, e.g. sys$scratch:test_ (the program will append 0000.TIF, 0001.TIF etc afterwards) Or enter (possibly with middle-mouse-click): "DK0:[MICROCT.DATA.00001234.00003456]ANIMATION_" to have the result go to the measurement directory.
:* Click on the 'Auto-Print' box. Then 'ok'
:* Adjust the number of views (e.g. 200), then click on 'Start Calculation', and it will render. This may well take a long time.
:* Take those TIFF files to your PC, and combine the sequences in the program that you are using to convert the TIFF files to AVI or MOV files (like Windows Movie Maker 2, or Quick Time Pro, or Adobe Premiere etc.) 

<b>Notes/Hints:</b>
:* The order in the above list can also be reversed: You can first set up the 'Auto-Print', and then go into the 'Animation' menu, choose start and end settings, and hit 'Start Calculation'
:* The positions A and B can be any: e.g. with subdim, you can first take everything (A), then slide it back to nothing (B).
:* You can even slowly change the color of an object. Or slowly hiding objects: choose 'transparent' for object, but change from 0.0 (A) to 1.0 (B)
:* If you want to create a movie with different sections, e.g. first rotate around, then slowly make bone transparent, then cut in: Do this in multiple sections with the 3D program, e.g. first create Auto-Print files 'rotation_0000 to rotation_0200', then 'transp_0000 to transp_0050', and then 'cut_0000 to cut_0100'. Make sure ALL the settings from the last view of the previous section match those of the first view of the next section so you get smoot transitions.
:* The 'Auto-Print' box is also usable without the 'Animation' Menu: Activate it, Like above, with sys$scratch:test_ only the beginning of filename. 'ok' Then, whenever a 3D image is completely built-up (so when you are happy with a view and you do not interrupt the build-up), automatically a TIF file is generated, numbered sequentially.


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===Combine two volumes to create transparent image===

First create your two start "seg.aim" images
Start by running either the normal eval, or $ voi to get one _seg.aim file of one region

Rename it to a better name in the session manager, e.g. c0001234_all.aim

Then either by choosing different contours, or a different threshold, start the $ voi or the normal evaluation again, which will create another _seg.aim file.

Load them in the 3D viewer ('all files') to check that they look like expected.

Now we will go into IPL and concatenate those two volumes.

<pre>
$ ipl
/read all xx_all.aim
/read trab xx_seg.aim
/transparent
  -input_solid               trab
  -input_transp              all
  -output                    out
</pre>

Note: the solid volume is OVERWRITING the transparent input volume, so usually, it
is the smaller (inner) of the two.

<pre>
/write out xxx_transp.aim
/quit
</pre>

Then load the _transp.aim file in 3D, go to 3D program FAQ to see how to change transparency levels in the Display options there.

See IPL FAQ or 3D program FAQ if you need help with these parts.

<b>Step by Step Example:</b> Showing your chosen trab VOI within whole bone
:* $ voi, enter threshold in ipl_voi.com, start 3d eval WITHOUT contours
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_all.aim
:* Start up normal eval program, draw trabecular contours, check threshold in ipl_fixed_batch_v4.com, start 3D eval.
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished 

<b>Step by Step Example:</b> Showing high-dense volume surronded by lower density volume

:* Start normal 3D eval with HIGH threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* Rename xxxx_seg.aim to xxxx_high.aim
:* If wished: read out 3d result database with $ uct_list
:* Start normal 3D eval with LOW threshold entered in ipl_fixed_batch_v4.com
:* WAIT UNTIL THE JOB IS FINISHED!
:* go into ipl and combine the two, see code above
:* Voila, finished


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==Image Tours==
===XtremeCT Image Tours===

===MicroCT Image Tours===
*Refer to [[Media:Tours_image_gallery.pdf|'''MicroCT Image Gallery''']] with its [[Media:Tours_image_notes.pdf|'''Image Notes''']].
*Refer to [https://youtu.be/tT3dz4VrwfE '''MicroCT Image Tour YouTube Video''']
*Hover over a thumbnail and click on its overlaid description to see the animated GIF or a larger version of the image.


<gallery mode="packed-hover" heights=220px caption="Micro-CT Scans">
Image:MOUSE_SKELETON_PIC01.jpg|[[Media:MOUSE_SKELETON_360.gif|Mouse (38µm)]]
Image:Segmented_Mouse_Femur.jpg|[[Media:Segmented_Mouse_Femur.jpg|Mouse Femur showing Cortical and Trabecular Bone (10µm)]]
Image:LIZARD_WHOLE_VIEW_P1_0044.jpg|[[Media:LIZARD_SKELETON_360.gif|Lizard (88µm)]]
Image:LIZARD_SKULL.jpg|[[Media:LIZARD_SKULL.jpg|Lizard Skull showing Thickness Distribution (25µm)]]
Image:DUCK_BEAK_PIC01.jpg|[[Media:DUCK_BEAK_360.gif|Duck Beak (60µm) Courtesy of Dr. A. Iwaniuk]]
Image:Human_Tooth.jpg|[[Media:Human_Tooth.jpg|Human Tooth (30µm) Courtesy of Dr. C. Stewart]]
Image:PINECONE_TH_PIC05.jpg|[[Media:PINECONE_360.gif|Pinecone showing Thickness Distribution (69µm)]]
Image:SHELL01_SEG_PIC01.jpg|[[Media:SEASHELL_360.gif|Seashell (50µm)]]
Image:TURTLE_SKULL.jpg|[[Media:TURTLE_SKULL_360.gif|Turtle Skull (60µm)]]
Image:SAND_DOLLAR.jpg|[[Media:SAND_DOLLAR.jpg|Sand Dollar (37µm)]]
Image:MOUSE_L1-L6.jpg|[[Media:MOUSE_SPINE_SEG_360.gif|Mouse Spine showing Cortical and Trabecular Bone (10µm)]]
Image:MOLAR.jpg|[[Media:MOLAR.gif|Human Tooth (60µm) Courtesy of Dr. C. Stewart]]
</gallery>


<gallery mode="packed-hover" heights=220px caption="Contrast-Enhanced Micro-CT Scans">
Image:Contrast_mouse_head_XZ_thumb.jpg|[[Media:Contrast mouse head XZ.jpg|Mouse Head (60µm, XZ plane)]]
Image:Contrast_mouse_head_XY_thumb.jpg|[[Media:Contrast mouse head XY.jpg|Mouse Head (60µm, XY plane)]]
Image:Contrast_mouse_head_YZ_thumb.jpg|[[Media:Contrast mouse head YZ.jpg|Mouse Head (60µm, YZ plane)]]
</gallery>


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==Extract Results==
===Automatic Results===
Results are generally automatically extracted after each analysis to the UCT_RESULTS directory.<br>  
The results files have the form of: 
*UCT_LIST_*''PROJECT''*.TXT for XtremeCTs: e.g. result file UCT_LIST_KYLA.TXT for the following project.
*UCT_LIST_3DLOG_*''PROJECT''*.TXT for microCTs: e.g. result file UCT_LIST_3DLOG_KYLA.TXT for the following project.
*where ''PROJECT'' is specified in the evaluation tool script setup.
[[File:Script_modify_basic_project.jpg|500px]]

Open the result file and copy and paste it into Excel, e.g.
<pre>
$ dir uct_results:*kyla*
$ eve uct_results:UCT_LIST_3DLOG_KYLA.TXT
</pre>
 
Or transfer the file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].  
*microct/vivact account UCT_RESULTS location:    ADISK1:[MICROCT.RESULTS]
*invivo/invitro account UCT_RESULTS location:    ADISK1:[BONELAB.RESULTS]


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===Extract Results from XtremeCT Database using UPAT_LIST===
*Run <code>$ UPAT_LIST</code> to take in a range of samples and extract the standard patient results, which may include scans from other projects.
**Run <code>$ UPAT_LIST -h</code> to print out help for all parameters. 
**For standard analysis on XtremeCT2, the default Evaluation Type 4=XT1 is not applicable. To get results for XtremeCT2, you need to run upat_list twice.  Once for evaluation 5 and once for 6.
<pre>   Evaluation type (1-6) [4]:   Type code of evaluation (4=XT1, 5=trabecular, 6=cortical, default=4) </pre>


*Run <code>$ @com:EXTRACT_UPAT_LIST</code> to take in a list of sample numbers and extract the standard patient results with follow-ups and append them to a result file.  
<pre>
$ @COM:EXTRACT_UPAT_LIST P1 P2 P3 P4 P5

    P1 = Sample List
    P2 = Site (RR, RL, TR, TL, R*, T*, *)
    P3 = Number of Follow-Ups (max 19)
    P4 = Results Output File
    P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST mysamples.txt * 19 myresults.txt 5
</pre>


*Run <code>$ @com:EXTRACT_UPAT_LIST_NOMATCH</code> to take in a list of sample numbers and extract the standard patient results without matching follow-ups and append them to a result file.  
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH P1 P2 P3 P4 P5

    P1 = Sample List
    P2 = Site (RR, RL, TR, TL, R*, T*, *)
    P3 = Number of Follow-Ups (max 19)
    P4 = Results Output File
    P5 = Eval type (4=XT1, 5=Trab, 6=Cort)
</pre>

:An example to extract all sites:
<pre>
$ @com:EXTRACT_UPAT_LIST_NOMATCH mysamples.txt * 19 myresults.txt 5
</pre>


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===Extracts Results from microCT Database using UCT_LIST===
*Run <code>$ UCT_LIST</code> to take in a range of samples and extract the results, by specifying the first and last measurement numbers for the range they want to extract
*This may include scans results from other projects, but you can delete unrelated results that are extracted afterwards.
*The program will output a tab-delimited text file, which can be read into Excel or other analysis programs.
<pre>
$ uct_list

     UCT_LIST.EXE Version V5.22
     Template-File [UCT_3D_LIST_SHEET]:         !Press Enter to use the default results sheet.
     Output-File [SYS$SCRATCH:UCT_EVAL.TXT]:    !Enter a filename, e.g., BUIE_RESULTS.TXT.
     Density units (0 default) [0]:             !Press Enter.
     From Meas. # [0]:                          !Enter the first measurement number, e.g., 100.
     To Meas. #   [0]:                          !Enter the last measurement number, e.g., 101.  

Processing measurement 100
Processing measurement 101
</pre>
*An example output file: [[Media:Buie_results.xlsx|Buie_results.txt]]
*Or Run <code>$ @com:extract_results.com</code>

*References of results template: 
:*Formatted [[Media:Results_template_uct_list.xlsx|Excel template 1]] for results extracted with uct_list.
:*Formatted [[Media:Results_template_extract_results.xlsx|Excel template 2]] for results extracted with extract_results.com.
:*In vivo spreadsheet template for UCT data: [[Media:In vivo results template.xls| In vivo results template.xls]]
:*In vitro spreadsheet template for UCT data: [[Media:In vitro results template.xls| In vitro results template.xls]]


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===Understand Morphological Parameters===
*Refer to [[Media:Reference_Document_-_Parameters_from_upat_list.doc|'''Explanation of UPAT_LIST Output''']] to understand the result file.
*Refer to [[Media:Reference_Document_-_Parameters_from_uct_list.doc|'''Explanation of UCT_LIST Output''']] to understand the result file.


All values are determined on a slice-by-slice basis, then averaged over all the slices to calculate morphological results:

:*BV/TV -> Sum all raw data within the GOBJ and divide by 1200 mg/cc HA
:*Tb.N  -> As per standard method
:*Tb.Th and Tb.Sp -> Derived from BV/TV and Tb.N above (semi-derived method)
:*D100  -> Average density of entire cross section
:*DTrab -> Average density of trabecular region
:*Ct.Th -> Cortical area (from seg) divided by circumference (from GOBJ)
:*GOBJ circumference can be determined with /gobj_circum.

<pre>
BV/TV  -> VOX-BV/TV
BS/BV  -> TRI-BS/BV
Tb.Th  -> DT-Tb.Th
Tb.Sp  -> DT-Tb.Sp
Tb.N   -> DT-Tb.N
ConnD  -> Conn-Dens
SMI    -> TRI-SMI
DA     -> TRI-DA
</pre>

Usually I'd use the names on the left for the plots, but these correspond to the names on the right of the arrow in the Scanco output files.

<b>Note</b>, if you use the TRI-Tb.Th rather than the DT-Tb.Th*, then you are using the derived (plate-model) morphological parameters.  These are less accurate than the direct parameters.  They are calculated by triangulating the surface (marching cubes) to get BS, and then calculate thickness
Th = 2 * BV / BS, etc...

'''Mean Values'''
<pre>
mean 1: mean of bone AND marrow --> 'apparent density'
mean 2: mean of what was considered bone only (i.e. what was segmented) 
'bone tissue density'
</pre>

Note, there are five possible categories for the mean Mu.  They are assigned by setting <code>-region_number</code> in the <code>/voxgobj_scanco_param</code> function.  The region number is zero-based, so setting it to 0 corresponds to mean1, 1 corresponds to mean2, etc.  So, although mean1 and mean2 are typically apparent and tissue density, respectively, this can be adjusted in the IPL script by setting the region_number.  Mean3 might be useful for storing cortical bone density, for example.

<pre>
/voxgobj_scanco_param      Voxel or Mu Scanco Parameters
  -input                     Gray scale or Segmented AIM object
  -gobj_filename             GOBJ: input or Automatic
  -peel_iter                 Peel Iterations or Automatic
  -region_number             Region number for Mu only

! -region_number             0   ! mean1
! -region_number             1   ! mean2
! -region_number             2   ! mean3
! -region_number             3   ! mean4
! -region_number             4   ! mean5
</pre>

<b>What you should also know</b>: because of partial voluming effects, for Mean2, we are DISCARDING the 2 surface voxels of EVERY trabeculae - thus, to get meaningful Mean2, you have to do your scan with the chosen resolution high enough, such that the mean trabeculae is depicted by at the very least 5 pixels, better actually more than 6 pixels thickness. (You can do this check at the end in the XLS sheet: divide DT-Tb.Th* by el-size-mm.x, and you need to get numbers bigger than 6 or 7 or 10 or so.

For parameters such as ConnD where no GOBJ is taken as input, the TV is determined from the processing log stored in an AIM that has previously had a GOBJ applied (stored as the relative region of interest; ROI).  So, it is important to apply a GOBJ prior to ConnD measurements to ensure the TV is correctly determined (and not taken as the whole AIM).

'''Trabecular Number (TbN)'''
The epsilon values can be set to account for differences in scanner resolution, and hence 'surface roughness' for individual pixel suppression.

For microct, for good resolution: if there is a pixel 'sticking out' from a flat surface we do not assign that pixel with a thickness value of 1, but we let it 'get eaten' by the bigger sphere that sits in the center of the trabeculae. So this is nice for 'noise'  (0.9/1.5). 

For XT resolution, where also many 'good' features are just one or two pixels wide, I liked a lower epsilon value better (0.9/0.5).


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==Generate Report==
===Generate Standard Patient Report===
The standard patient reports are extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.  
*The number of follow-ups specified will determine if a baseline or follow-up report is generated.

<pre>
$ upat_list

     Mode (1 = list, 2 = print, 3 = show) [1]:  2
     Patient # (1-3162) [1]:                    !input the patient's sample number
     Site (found RR) [RR]:	                !RR or RL or TR or TL
     Maximum # of follow-ups (0-19) [19]:	!0 for baseline report, press return for follow-ups
     Template file [default]:	                !press return to use the default template
     Output filename [SYS$SCRATCH:UPAT...]:	!default output file (with sample number and the site) goes to sys$scratch
     # copies [1]:	                        !the number of printouts, 0 if no printout is desired
</pre>


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===Generate CaMos Patient Report===
The [http://www.camos.org '''CaMos'''] patient report is extracted from a DEC terminal using upat_list in print mode, which will print to a postscript (PS) file and can also print a hard copy.  
*To ensure the report is generated using the appropriate normative results, the patient's sample remarks should be in the form "F-RHRF" where the first character indicates the sex of the individual, otherwise the patient is assumed to be male.
<pre>
$ upat_list

     Mode (1 = list, 2 = print, 3 = show) [1]:  2
     Patient # (1-3162) [1]:                    !input the patient's sample number
     Site (found RR) [RR]:	                !RR or RL or TR or TL
     Maximum # of follow-ups (0-19) [19]:	!0 - 1st scan, 1 - 2nd scan, 2 - 3rd scan...press return for latest scan report 
     Template file [default]:	                COM:UPAT_EVAL_CAMOS.PS
     Output filename [SYS$SCRATCH:UPAT...]:	!default output file (with sample number and the site) goes to sys$scratch
     # copies [1]:	                        !the number of printouts, 0 if no printout is desired
</pre>


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===Print out report sheets===

The postscript report sheets can be generated and printed on the command line.  For the XtremeCT system, use <code>UPAT_PRINT_LIST.EXE</code> which can be run (using the symbol):
<pre>
$ UPAT_LIST
</pre>

Look in the UU: directory to see options for the template files (UPAT*.TXT) and the postscript output files (*.PS).
:* UU:UPAT_EVAL_FUP05_SCUSA.PS
:* UU:UPAT_EVAL_BASELINE_SCUSA.PS

For other options, see the upat_list help:
<pre>
$ UPAT_LIST -h
</pre>

One particular option that may be useful, is to turn off slice matching:
<pre>
$ UPAT_LIST -nomatch
</pre>

Here is an example of producing a report for the third measurement of TL for a patient, where we want only the most recent results in the report, without slice matching:
<pre>
$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=UU:UPAT_EVAL_BASELINE_SCUSA.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_0fu.ps

$ upat_list -b=3818 -e=3818 -s=TL -mb=01-MAY-2018 -me=01-AUG-2018 -nomatch -t=DISK1:[MICROCT.COMMANDS]UPAT_EVAL_CAMOS.PS -c=0 -o=sys$scratch:upat_pat_3818_tl_camos.ps
</pre>
The first command line generates a normal Scanco report, and the second command line generates a CAMOS report.

For reports from non-patient measurements (i.e., the vivaCT system or non-patient scans on the XtremeCT), the template files are different (UCT*.TXT) and the postscript outputs are different (UCT*.PS). To print a result sheet use:
<pre>
$ RUN UM:UCT_RAY_BATCH.EXE
</pre>

If you want to create a postscript file, but not send it to the printer, set the number of copies to zero (interactive).  Then, find the postscript file from the <code>SYS$SCRATCH</code> directory and transfer it to your PC.  You must transfer the postscript file in ASCII mode.  The files are typically called TEMP_3D.PS or UPAT_PAT_62_RR.PS.  A program such as Adobe Photoshop can convert the postscript file to a different format.

See also our custom scripts:
<pre>
$ @COM:PRINT_2D.COM
$ @COM:PRINT_3D.COM
</pre>


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===Convert PS to PDF report===
The report can be converted to PDF using <code>$ @SCOM:PS_TO_PDF</code>  by:

#Follow the instructions above for creating a report, using "2" to print and "0" for the number of copies. (Use the default template file and output filename.)
#Locate the file on the sys$scratch by <code>$ cd sys$scratch</code> and <code>$ dir</code>
#*The file should read "UPAT_PAT_[sample #]_[site].PS;1" (e.g. UPAT_PAT_0010_RL.PS;1)
#*You can view this file on the monitor by typing <code>$ gs UPAT_PAT_0010_RL.PS;1</code>
#Convert the postscript to PDF by typing in the command followed by the .PS file to convert <pre>$ @SCOM:PS_TO_PDF  UPAT_PAT_0010_RL.PS;1</pre>
#The PDF file can then be located again in the sys$scratch directory.  

You can transfer the result file to your computer using [[Scanco_User_Instructions#How_to_FTP_files|'''FTP''']].


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