Registration - Revision history

Tom Sgouros: Most of these instructions have changed, and the linked page has the updated version.

2014-04-09T21:13:52Z

Most of these instructions have changed, and the linked page has the updated version.

← Older revision		Revision as of 21:13, 9 April 2014
Line 1:		Line 1:
	[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. It must have the format: E#####_scan; where # is substituted with a digit. Import files/folders from Bioengineering:~~		[[Registration of Bones Across Positions#Technical Notes\|Use instructions here]]
	~~#* <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 <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 <code>crop_values.txt</code> file.~~
	~~#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, <code>unixbatch.sh</code>, and <code>batchgen.cfg</code>.~~
	~~## The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm.~~
	~~## The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program.~~
	~~## The <code>regbatch.list</code> file contains a list~~ of ~~<code>WristRegistration</code> commands.~~
	#~~# The configuration file <code>batchgen.cfg</code> contains the parameters used for this run.~~
	~~<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>~~
	~~#Run <code>unixbatch.sh</code> from the top level of the subject directory.~~
	~~#* This should go through and run all the major steps.~~
	~~#* <code>./unixbatch.sh</code>~~
	~~#After <code>unixbatch.sh</code> finishes, you need to validate the output of the registration steps~~
	#* Use ~~<code>WristVis</code> to check the registration~~
	~~#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.~~
	#Folders <code>collected_results</code> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results

Brad Berg at 14:09, 22 May 2009

2009-05-22T14:09:09Z

← Older revision		Revision as of 14:09, 22 May 2009
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	#* Run it from the top level of the subject directory.		#* 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 <code>crop_values.txt</code> file.		#* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the <code>crop_values.txt</code> file.
	#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, ~~and~~ <code>unixbatch.sh</code>.		#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, <code>unixbatch.sh</code>, and <code>batchgen.cfg</code>.
	## The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm.		## The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm.
	## The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program.		## The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program.
	## The <code>regbatch.list</code> file contains a list of <code>WristRegistration</code> commands.		## The <code>regbatch.list</code> file contains a list of <code>WristRegistration</code> commands.
			## The configuration file <code>batchgen.cfg</code> contains the parameters used for this run.
	<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>		<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
	#Run <code>unixbatch.sh</code> from the top level of the subject directory.		#Run <code>unixbatch.sh</code> from the top level of the subject directory.

Brad Berg at 13:29, 21 May 2009

2009-05-21T13:29:53Z

← Older revision		Revision as of 13:29, 21 May 2009
Line 8:		Line 8:
	#* Run it from the top level of the subject directory.		#* 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 <code>crop_values.txt</code> file.		#* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the <code>crop_values.txt</code> file.
	#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, and <code>unixbatch.sh</code>. The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm. The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program. The <code>regbatch.list</code> file contains a list of <code>WristRegistration</code> commands.		#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, and <code>unixbatch.sh</code>.
			## The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm.
			## The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program.
			## The <code>regbatch.list</code> file contains a list of <code>WristRegistration</code> commands.
	<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>		<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
	#Run <code>unixbatch.sh</code> from the top level of the subject directory.		#Run <code>unixbatch.sh</code> from the top level of the subject directory.

Brad Berg at 19:12, 20 May 2009

2009-05-20T19:12:53Z

← Older revision		Revision as of 19:12, 20 May 2009
Line 8:		Line 8:
	#* Run it from the top level of the subject directory.		#* 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 <code>crop_values.txt</code> file.		#* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the <code>crop_values.txt</code> file.
	#* <code>batchGen.pl</code> ~~should create~~ three files: <code>regbatch</code>, <code>subsetbatch</code>, and <code>unixbatch</code>. <code>unixbatch</code> ~~is the master file that calls~~ the other two. <pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>		#* The script <code>batchGen.pl</code> creates three files: <code>regbatch.list</code>, <code>subsetbatch.list</code>, and <code>unixbatch.sh</code>. The script <code>unixbatch.sh</code> uses the other two files to dispatch commands in parallel to a processor farm. The <code>subsetbatch.list</code> has a set of commands invoking the <code>subset</code> program. The <code>regbatch.list</code> file contains a list of <code>WristRegistration</code> commands.
	#Run <code>unixbatch</code> from the top level of the subject directory.		<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
			#Run <code>unixbatch.sh</code> 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.
	#* <code>./unixbatch</code>		#* <code>./unixbatch.sh</code>
	#After <code>unixbatch</code> finishes, you need to validate the output of the registration steps		#After <code>unixbatch.sh</code> finishes, you need to validate the output of the registration steps
	#* Use <code>WristVis</code> to check the registration		#* Use <code>WristVis</code> to check the registration
	#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.		#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
	#Folders <code>collected_results</code> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results		#Folders <code>collected_results</code> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results

Brad Berg at 18:11, 20 May 2009

2009-05-20T18:11:54Z

← Older revision		Revision as of 18:11, 20 May 2009
Line 7:		Line 7:
	#Run <code>batchGen.pl</code> 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.		#* 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.		#* The first time you run it, run with the <code>--crop</code> option, so it imports the data from the <code>crop_values.txt</code> file.
	#* <code>batchGen.pl</code> should create three files: <code>regbatch</code>, <code>subsetbatch</code>, and <code>unixbatch</code>. <code>unixbatch</code> is the master file that calls the other ~~three~~		#* <code>batchGen.pl</code> should create three files: <code>regbatch</code>, <code>subsetbatch</code>, and <code>unixbatch</code>. <code>unixbatch</code> is the master file that calls the other two. <pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
	<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
	#Run <code>unixbatch</code> from the top level of the subject directory.		#Run <code>unixbatch</code> 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.

Brad Berg at 16:38, 20 May 2009

2009-05-20T16:38:19Z

← Older revision		Revision as of 16:38, 20 May 2009
Line 16:		Line 16:
	#* Use <code>WristVis</code> to check the registration		#* Use <code>WristVis</code> to check the registration
	#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.		#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> option, and choose NOT to re-run all parts. Then let it hopefully help you through the process.
	#Folders <code>collected_results</~~cdoe~~> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results		#Folders <code>collected_results</code> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results

Brad Berg at 16:37, 20 May 2009

2009-05-20T16:37:59Z

← Older revision		Revision as of 16:37, 20 May 2009
Line 8:		Line 8:
	#* Run it from the top level of the subject directory.		#* 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.		#* 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		#* <code>batchGen.pl</code> should create three files: <code>regbatch</code>, <code>subsetbatch</code>, and <code>unixbatch</code>. <code>unixbatch</code> is the master file that calls the other three
	<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>		<pre>E06001_scan> $G/install_linux/bin/wrist/batchGen.pl --crop</pre>
	#Run unixbatch from the top level of the subject directory.		#Run <code>unixbatch</code> 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		#* <code>./unixbatch</code>
	#After unixbatch finishes, you need to validate the output of the registration steps		#After <code>unixbatch</code> finishes, you need to validate the output of the registration steps
	##Use WristVis to check the registration		#* Use <code>WristVis</code> 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.		#* If there are errors, re-run <code>batchGen.pl</code>, without the <code>--crop</code> 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		#Folders <code>collected_results</cdoe> and <code>auto_registr_resuls</code> contain the same registration results in different formats, whereas <code>classified_scans</code> contains the tissue classification results

Brad Berg at 16:32, 20 May 2009

2009-05-20T16:32:49Z

← Older revision		Revision as of 16:32, 20 May 2009
Line 1:		Line 1:
	[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 ~~[EXXXXX_scan] & import~~ files/folders from Bioengineering:		#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]		#* <code>original_scans/</code> CT_Scans [scans of all wrist positions]
	##original_stacks/ [segmented neutral position of wrist]		#* <code>original_stacks/</code> [segmented neutral position of wrist]
	##crop_values.txt		#* <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.
	#~~#should always be run~~ from the top level of the subject directory		#* Run it from the top level of the subject directory.
	#~~#the~~ first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.		#* 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		#* batchGen.pl should create three files: regbatch, subsetbatch, & unixbatch. unixbatch is the master file that calls the other three
	##/~~map~~/~~gfx0/data~~/wrist~~/batchfiles/linuxconvert~~/batchGen.pl --crop		<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

Brad Berg at 14:08, 20 May 2009

2009-05-20T14:08:33Z

← Older revision		Revision as of 14:08, 20 May 2009
Line 2:		Line 2:

	#Create the subject directory [EXXXXX_scan] & import files/folders from Bioengineering:		#Create the subject directory [EXXXXX_scan] & import files/folders from Bioengineering:
	##CT_Scans [scans of all wrist positions]		##original_scans/ CT_Scans [scans of all wrist positions]
	##original_stacks [segmented neutral position of wrist]		##original_stacks/ [segmented neutral position of wrist]
	##crop_values.txt		##crop_values.txt
	#Run batchGen.pl to create the master batch files		#Run batchGen.pl to create the master batch files

Eni Halilaj at 17:52, 7 May 2009

2009-05-07T17:52:03Z

← Older revision		Revision as of 17:52, 7 May 2009
Line 1:		Line 1:
	[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]

	#~~Upload all Files and create~~ the subject directory ~~(this is done)~~		#Create the subject directory [EXXXXX_scan] & import files/folders from Bioengineering:
	#Run batchGen.pl to create the master batch files~~- (you should start here)~~		##CT_Scans [scans of all wrist positions]
	~~##located for now at: /map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl~~		##original_stacks [segmented neutral position of wrist]
			##crop_values.txt
			#Run batchGen.pl to create the master batch files
	##should always be run from the top level of the subject directory		##should always be run from the top level of the subject directory
	##the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.		##the first time you run it, run with the --crop option, so it imports the data from the crop_values.txt file.
Line 14:		Line 16:
	##Use WristVis to check the registration		##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.		##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