Registration: Difference between revisions
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[https://wiki.brown.edu/confluence/display/orthobio/Compiling+the+CS+Carpal+Pipeline|Compiling the CS Carpal Pipeline] | [https://wiki.brown.edu/confluence/display/orthobio/Compiling+the+CS+Carpal+Pipeline|Compiling the CS Carpal Pipeline] | ||
#Create the subject directory | #Create the subject directory. It must have the format: E#####_scan; where # is substituted with a digit. Import files/folders from Bioengineering: | ||
# | #* <code>original_scans/</code> CT_Scans [scans of all wrist positions] | ||
# | #* <code>original_stacks/</code> [segmented neutral position of wrist] | ||
# | #* <code>crop_values.txt</code> | ||
#Run batchGen.pl to create the master batch files | #Run <code>batchGen.pl</code> to create the master batch files. | ||
# | #* Run it from the top level of the subject directory. | ||
# | #* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the crop_values.txt file. | ||
# | #* batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three | ||
<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre> | |||
#Run unixbatch from the top level of the subject directory. | #Run unixbatch from the top level of the subject directory. | ||
##This should go through and run all the major steps | ##This should go through and run all the major steps. | ||
##./unixbatch | ##./unixbatch | ||
#After unixbatch finishes, you need to validate the output of the registration steps | #After unixbatch finishes, you need to validate the output of the registration steps | ||
Revision as of 16:32, 20 May 2009
- Create the subject directory. It must have the format: E#####_scan; where # is substituted with a digit. Import files/folders from Bioengineering:
original_scans/CT_Scans [scans of all wrist positions]original_stacks/[segmented neutral position of wrist]crop_values.txt
- Run
batchGen.plto create the master batch files.- Run it from the top level of the subject directory.
- The first time you run it, run with the
--cropoption, so it imports the data from the crop_values.txt file. - batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop
- Run unixbatch from the top level of the subject directory.
- This should go through and run all the major steps.
- ./unixbatch
- After unixbatch finishes, you need to validate the output of the registration steps
- Use WristVis to check the registration
- If there are errors, re-run batchGen.pl, without the --crop option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
- Folders collected_results & auto_registr_resuls contain the same registration results in different formats, whereas classified_scans contains the tissue classification results