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New page: Compiling the CS Carpal Pipeline #Upload all Files and create the subject directory (this is done) #Run batchGen.pl to create the master batch files- (you should start here) ##located fo... |
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##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. | ||
##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 -- | ##/map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl --crop | ||
#This should go through and run all the major steps | #Run unixbatch from the top level of the subject directory. | ||
##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 | ||
##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. | ||
Revision as of 17:49, 7 April 2009
Compiling the CS Carpal Pipeline
- Upload all Files and create the subject directory (this is done)
- Run batchGen.pl to create the master batch files- (you should start here)
- located for now at: /map/gfx0/data/wrist/batchfiles/linuxconvert/batchGen.pl
- 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.
- 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
- 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
- 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.