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run_betfunc.py
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run_betfunc.py
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#!/usr/bin/env python
""" run_betfunc.py - run bet on functional images
USAGE: python run_betfnc.py <name of dataset> <basedir - default is staged>
"""
## Copyright 2011, Russell Poldrack. All rights reserved.
## Redistribution and use in source and binary forms, with or without modification, are
## permitted provided that the following conditions are met:
## 1. Redistributions of source code must retain the above copyright notice, this list of
## conditions and the following disclaimer.
## 2. Redistributions in binary form must reproduce the above copyright notice, this list
## of conditions and the following disclaimer in the documentation and/or other materials
## provided with the distribution.
## THIS SOFTWARE IS PROVIDED BY RUSSELL POLDRACK ``AS IS'' AND ANY EXPRESS OR IMPLIED
## WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND
## FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL RUSSELL POLDRACK OR
## CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
## CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
## SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON
## ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
## NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
## ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
import os
import sys
import launch_qsub
def main():
if len(sys.argv)>1:
ds=sys.argv[1]
else:
usage()
if len(sys.argv)>2:
basedir=sys.argv[2]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
basedir='/scratch/01329/poldrack/openfmri/staged/'
outfile=open('run_betfunc_%s.sh'%ds,'w')
found_files=0
for d in os.listdir(basedir+ds):
if d[0:3]=='sub':
for bd in os.listdir('%s/%s/BOLD/'%(basedir+ds,d)):
for m in os.listdir('%s/%s/BOLD/%s/'%(basedir+ds,d,bd)):
if m=='bold_mcf.nii.gz':
root='%s/%s/BOLD/%s/'%(basedir+ds,d,bd)
outfile.write('bet %s/%s %s/%s -F\n'%(root,m,root,m.replace('mcf','mcf_brain')))
found_files=1
outfile.close()
if found_files>0:
print 'now launching using:'
print 'launch -s run_betfunc_%s.sh -n betfunc -r 00:10:00'%ds
launch_qsub.launch_qsub(script_name='run_betfunc_%s.sh'%ds,runtime='00:10:00',jobname='%sbf'%ds,email=False)
else:
print 'no files found to process'
if __name__ == '__main__':
main()