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='/corral-repl/utexas/poldracklab/openfmri/staged' sk=load_scankey(os.path.join(basedir,ds,'scan_key.txt')) TR=sk['TR'] outfile=open('run_qa_%s.sh'%ds,'w') dsdir=os.path.join(basedir,ds) for d in os.listdir(dsdir): if d[0:3]=='sub': for bd in os.listdir('%s/%s/BOLD/'%(dsdir,d)): for m in os.listdir('%s/%s/BOLD/%s/'%(dsdir,d,bd)): if m=='bold_mcf.nii.gz': root='%s/%s/BOLD/%s/'%(dsdir,d,bd) outfile.write('fmriqa.py %s/%s %s\n'%(root,m,sk['TR'])) outfile.close() print 'now launching using:' print 'launch -s run_qa_%s.sh -n qa -r 00:30:00'%ds launch_qsub.launch_qsub(script_name='run_qa_%s.sh'%ds,runtime='00:30:00',jobname='%sqa'%ds,email=False)
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 = "/corral-repl/utexas/poldracklab/openfmri/staged" sk = load_scankey(os.path.join(basedir, ds, "scan_key.txt")) TR = sk["TR"] outfile = open("run_qa_%s.sh" % ds, "w") dsdir = os.path.join(basedir, ds) for d in glob.glob(os.path.join(dsdir, "sub*/BOLD/*/bold_mcf.nii.gz")): outfile.write("fmriqa.py %s %s\n" % (d, sk["TR"])) outfile.close() if float(sk["TR"]) < 2: queue = "largemem" ncores = 24 print "using largemem queue" else: queue = "normal" ncores = 12 print "now launching using:" print "launch -s run_qa_%s.sh -n qa -r 00:30:00" % ds launch_qsub.launch_qsub( script_name="run_qa_%s.sh" % ds, runtime="00:30:00", jobname="%sqa" % ds, email=False, queue=queue, ncores=ncores, )
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 = '/corral-repl/utexas/poldracklab/openfmri/staged' sk = load_scankey(os.path.join(basedir, ds, 'scan_key.txt')) TR = sk['TR'] outfile = open('run_qa_%s.sh' % ds, 'w') dsdir = os.path.join(basedir, ds) for d in glob.glob(os.path.join(dsdir, 'sub*/BOLD/*/bold_mcf.nii.gz')): outfile.write('fmriqa.py %s %s\n' % (d, sk['TR'])) outfile.close() if float(sk['TR']) < 2: queue = 'largemem' ncores = 24 print 'using largemem queue' else: queue = 'normal' ncores = 12 print 'now launching using:' print 'launch -s run_qa_%s.sh -n qa -r 00:30:00' % ds launch_qsub.launch_qsub(script_name='run_qa_%s.sh' % ds, runtime='00:30:00', jobname='%sqa' % ds, email=False, queue=queue, ncores=ncores)