Editing Archive (section)

==Project How To's==

===How To: Set up a new project===

:<i>Step 1: Make directories</i>
:* In DISK40:[DATA.UCT.PROJECTS] make a directory HERZOG.
:*Make COM, LOG, DOC directories. DOC can have IMG. IMG can have 2D and 3D.
:<i>Step 2: Copy files</i>
:* Copy some of the COM files from another project. Especially EVAL.COM and EVALUATION.COM.
:* EVAL.COM is the main file that calls EVALUATION.COM
:<i>Step 3: Create a symbol</i>
:* Go to: <code>cd DISK1:[UCT]</code>
:*Edit:<code> eve LOGIN.COM</code>
:* Add logical <code>HERZOG</code> in alphabetical order.
:* Add <code>EVAL_HERZOG :== @UCT-DATA-R:[HERZOG.COM]EVAL.COM HERZOG</code>
:* Type <code>rulog</code> to update the symbols.


===How To: Process a project===

:* Record specimens to be scanned on a project sheet.
:* Scan
:* Create directory in projects: COM, LOG, MODELS, DOC
:* Create EVAL.COM
:* Do evaluation (will move the output AIMs to the projects directory)
:* Backup RSQs.
:* Rename the AIMs and place in MODELS.
:* Backup AIMs fromUD (measurement disk). Note that we don’t backup ISQs. These can be made again from the RSQs and take much more disk space than the AIMs that have been cutout from them.
:* Generate 2D images.


===How To: Evaluate a project (PRE)===

:* This is done in 2 steps: AIM extraction, AIM filtration.
:*Run the evaluation as user XUCT so that enough memory can be allocated for the job. To login as xuct on blund, type <code>blund</code> (see HowTo:).
:* <code>EVAL_HERZOG G 245</code> (runs the evaluation, with option G, on sample 245).
:* When <code>uct_evaluation</code> tool pops up, click <code>cancel</code> to get sample 245.
:*Select the <evaluation 3D> button, select <ROI>, then <start evaluation>.
:*Then <code>exit</code>.
:*To look at the latest <code>UCT_EVALUATION.LOG</code>, go to <code>cd scratch</code>
:*Once the AIM has been successfully extracted (it’ll be located in the measurement directory), start the second part of the analysis by typing: <code>EVAL_HERZOG SE 245</code> or <code>EVAL_HERZOG 245</code>. With no options defaults to GSE, and since option G is already processed, it skips to options <code>SE</code>.
::- Option <code>S</code> starts SAP with which the user can check that the AIM captures the data of interest.
::- Once you exit from SAP, the file is Gaussian filtered (option <code>E</code> in script), renamed to the PROJECTS directory, and the original ISQ file in the measurement directory is deleted.
:*Once the two steps of evaluation are finished, the filtered aims should be renamed to meaningful project names (see renaming HowTo's).
:*If anything goes wrong in the evaluation, goto the LOG directory in the HERZOG project to see the problem.


===How To: Evaluate a project (POST)===

:*This is done typically once the original data has been pre-processed (i.e., cutout and filtered).
:* Create a script file with the exact name: <CODE>SUBMIT_ALL_IPL.COM</code>
::- This file usually contains references to various steps in the evaluation such as trabecular morphological evaluation, cortical evaluation, mask generation, etc. These might be named <code>TRAB</code>, <code>CORT</code>, <code>MASK</code> or, if all three steps are to be performed, use <code>ALL</code>.
:* Create an IPL procedure file (as opposed to interactive use of IPL). Remember to use the two dots (..) after the IPL procedure! This file might be named <code>IPL_TRAB_SUBMIT_ALL.COM</code> for example. One of these files is necessary for each of the possible evaluations (trab, cort, mask).
:* Test the procedures by submitting only one job.
::- From the <code>COM</code> directory, type <code>SAI TRAB NORMAL-01</code>. This will submit the file that contains the string <code>NORMAL-01</code> to be evaluated using the IPL procedure that <code>TRAB</code> refers to in the <code>SUBMIT_ALL_IPL.COM</code> file.
:* Submit the project for evaluation using <code>SAI ALL</code>. Or, if only one part of the evaluation is to be performed <code>SAI TRAB</code>.
:* Look in the <code>LOG</code> directory for the results from the evaluation.


===How To: Measure reconstruction angle and align an image axially===

:* The ISQ generated from the RSQ can be re-aligned axially.
:* Measure the reconstruction angle:
::- Start <code>uct_evaluation</code> and load the ISQ image.
::- Launch <code>corelut</code> from<code> uct_evaluation</code> (<code><lut></code>, <code><modify></code>, <code><option cursor></code>, <code> <position></code>).
::- Click <code><draw line></code> and <code><show></code>.
::- <code><shift></code> to draw line, <code><mb2></code> to store line (don’t forget to uncheck the show line button).
::- View reconstruction angle in corelut window. Follow right-hand rule.
:* Generate a new ISQ with: <code>fan_reko_all [directory] -12.6</code>


===How To: Rename the AIMs from the data base and move to MODELS===

:*Do this from the COM directory of the particular project: <code>ur michigan</code>
:* Type: <code>r2m 404 421</code> (these are the measurement numbers). Makes a file called REN2MODELS.COM.
:* if you want to rename also GOBJ + THRES + FILT aims, type <code>r2m ALL (+meas #)</code>
:*Edit the COM file. Change xx.yy to MICHIGAN (capitals). Change “right�? to “r�? and “left�? to “l�? so that all files are the same length.
:* @REN2MODELS.COM (moves the files to the MODELS directory).
:* Test that the AIMs were properly moved to the MODELS directory by typing: <code>dh0</code> (tests no files in 000... from projects directory).
:*Delete the empty directories: <code>dec0</code>


===How To: Create 2D or 3D images===

:*Always rename the images from their system-given name to a meaningful project name.
:* Manually, start <code>corelut</code>. Set colormap to black and white (#2). 
:<i>Option 1: Manual</I>
:*Start <code>sap</code> and <code>pwindows</code>. 
:<i>Option 2: Automatic</i>
:* Generate an SAP.COM file using <code>@ut:create_sap-pw.com </code>or “<code>csp</code>�?
:* Edit SAP.COM. Then start with <code>@SAP.COM XY</code>.
:* Make XY, YZ and XZ 2d images, and some detail images. Always close <code>pwindows</code> before <code>sap</code>. The next AIM will be automatically loaded.
:* Always save as TIFFs. Powerpoint is able to make invisible background with TIFFs only.
:* Rename the TIFF files to TIF (one ‘F’) so that programs such as Adobe Photoshop will recognize the files.
:* Look at TIFFs using <code>xv filename</code> or <code>i disp filename</code> (image magick).


===How To: Compile LOG files from IPL evaluation===

:*Concatenate the log files into one long file and place it in the log directory.
::- <code>app/new ipl_trab*.log [-.doc]calgary_bear_trab.log</code>
:*In the doc directory, use the tabulating program to extract the results.
::- <code>taball calgary_bear</code> (it looks for a file ending in ‘<code>_trab</code>’ extension).
:*Instead of <code>taball</code>, individual IPL evaluation results can be tabulated. Type <code>tab</code> to get the usage.