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'
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='/scratch/01329/poldrack/openfmri/staged/'
if len(sys.argv)>3:
wait_process=int(sys.argv[3])
else:
wait_process=[]
outfile=open('run_betfunc_%s.sh'%ds,'w')
found_files=0
dsdir=os.path.join(basedir,ds)
for d in glob.glob(os.path.join(dsdir,'sub*/BOLD/*/bold.nii.gz')):
outfile.write('bet %s %s -F\n'%(d.replace('.nii','_mcf.nii'),d.replace('.nii','_mcf_brain.nii')))
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,hold=wait_process)
else:
print 'no files found to process'
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/'
outfile=open('run_mcflirt_%s.sh'%ds,'w')
boldfiles=glob.glob(os.path.join(basedir,ds,'sub*/BOLD/*/bold.nii.gz'))
if len(boldfiles)==0:
print 'no bold files found!'
return
for d in boldfiles:
outfile.write('mcflirt -in %s -sinc_final -plots\n'%d)
outfile.close()
print 'now launching using:'
print 'launch -s run_mcflirt_%s.sh -n mcflirt -r 00:30:00'%ds
launch_qsub.launch_qsub(script_name='run_mcflirt_%s.sh'%ds,runtime='00:30:00',jobname='%smcf'%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='/scratch/01329/poldrack/openfmri/staged/'
outfile=open('run_mcflirt_%s.sh'%ds,'w')
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.nii.gz':
root='%s/%s/BOLD/%s/'%(basedir+ds,d,bd)
outfile.write('mcflirt -in %s/%s -sinc_final -plots\n'%(root,m))
outfile.close()
print 'now launching using:'
print 'launch -s run_mcflirt_%s.sh -n mcflirt -r 00:30:00'%ds
launch_qsub.launch_qsub(script_name='run_mcflirt_%s.sh'%ds,runtime='00:30:00',jobname='%smcf'%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/'
outfile = open('run_mcflirt_%s.sh' % ds, 'w')
boldfiles = glob.glob(os.path.join(basedir, ds, 'sub*/BOLD/*/bold.nii.gz'))
if len(boldfiles) == 0:
print 'no bold files found!'
return
for d in boldfiles:
outfile.write('mcflirt -in %s -sinc_final -plots\n' % d)
outfile.close()
print 'now launching using:'
print 'launch -s run_mcflirt_%s.sh -n mcflirt -r 00:30:00' % ds
#launch_qsub.launch_qsub(script_name='run_mcflirt_%s.sh'%ds,runtime='00:30:00',jobname='%smcf'%ds,projname='Analysis_Lonestar',email=False)
launch_qsub.launch_qsub(script_name='run_mcflirt_%s.sh' % ds,
runtime='00:30:00',
jobname='%smcf' % ds,
email=False)
def main():
if len(sys.argv)>2:
taskid=sys.argv[1]
modelnum=int(sys.argv[2])
else:
usage()
if len(sys.argv)>3:
basedir=sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
basedir=os.path.abspath(os.curdir)
if len(sys.argv)>4:
tasknum=int(sys.argv[4])
else:
tasknum=0
if not basedir[-1]=='/':
basedir=basedir+'/'
if not os.path.exists(os.path.join(basedir,taskid,'group')):
os.mkdir(os.path.join(basedir,taskid,'group'))
if not os.path.exists(os.path.join(basedir,taskid,'group/model%03d'%modelnum)):
os.mkdir(os.path.join(basedir,taskid,'group/model%03d'%modelnum))
featdirs=[]
subdirs={}
cond_key=load_condkey(basedir+taskid+'/models/model%03d/condition_key.txt'%modelnum)
ntasks=len(cond_key)
print 'found %d tasks'%ntasks
fsfnames=[]
if tasknum==0:
tasks=range(1,ntasks+1)
else:
tasks=[tasknum]
for t in tasks:
f=mk_level3_fsf(taskid,t,modelnum,basedir)
for i in f:
fsfnames.append(i)
outfile=open('run_all_level3_%s.sh'%taskid,'w')
for f in fsfnames:
outfile.write('feat %s\n'%f)
outfile.close()
print 'now launching using:'
print 'launch -s run_all_level3_%s.sh -n %sl3 -r 01:00:00'%(taskid,taskid)
launch_qsub.launch_qsub(script_name='run_all_level3_%s.sh'%taskid,runtime='01:00:00',jobname='%sl3'%taskid,email=False)
def main():
artimes = ['08:00:00', '12:00:00', '24:00:00']
if len(sys.argv) > 1:
dataset = sys.argv[1]
else:
usage()
if len(sys.argv) > 2:
arlevel = int(sys.argv[2])
else:
arlevel = 1
print 'assuming autorecon 1 (skullstrip)'
if len(sys.argv) > 3:
basedir = sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!' % basedir
sys.exit(1)
else:
basedir = '/corral-repl/utexas/poldracklab/openfmri/staged/'
if len(sys.argv) > 4:
subdir = sys.argv[4]
if not os.path.exists(basedir):
print 'basedir %s does not exist!' % basedir
sys.exit(1)
else:
subdir = '/corral-repl/utexas/poldracklab/openfmri/subdir/'
print 'assuming subdir: %s' % subdir
outfile = open('run_autorecon%d_%s.sh' % (arlevel, dataset), 'w')
cmdctr = 0
for d in glob.glob(
os.path.join(basedir, dataset, 'sub*/anatomy/highres001.nii.gz')):
subnum = int(d.split('/')[-3].replace('sub', ''))
outfile.write('recon-all -autorecon%d -subjid %s_sub%03d -sd %s\n' %
(arlevel, dataset, subnum, subdir))
cmdctr += 1
outfile.close()
print 'now launch using:'
print 'launch -s run_autorecon%d_%s.sh -n %sar%d -r %s' % (
arlevel, dataset, dataset, arlevel, artimes[arlevel - 1])
launch_qsub.launch_qsub(script_name='run_autorecon%d_%s.sh' %
(arlevel, dataset),
runtime=artimes[arlevel - 1],
jobname='%sar%d' % (dataset, arlevel),
email=False,
parenv='1way',
ncores=cmdctr * 12)
def main():
if len(sys.argv)>2:
taskid=sys.argv[1]
modelnum=int(sys.argv[2])
else:
usage()
if len(sys.argv)>3:
basedir=sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
basedir=os.path.abspath(os.curdir)
if not basedir[-1]=='/':
basedir=basedir+'/'
outfile=open('run_all_level2_%s.sh'%taskid,'w')
featdirs=[]
subdirs={}
for d in os.listdir(basedir+taskid):
if d[0:3]=='sub':
for m in os.listdir('%s/%s/model/model%03d/'%(basedir+taskid,d,modelnum)):
if m[-5:]=='.feat':
featdirs.append(m)
fs=featdirs[-1]
subnum=int(d.replace('sub',''))
if not subdirs.has_key(subnum):
subdirs[subnum]={}
runnum=int(fs.split('_')[1].split('.')[0].replace('run',''))
tasknum=int(fs.split('_')[0].replace('task',''))
if not subdirs[subnum].has_key(tasknum):
subdirs[subnum][tasknum]=[]
subdirs[subnum][tasknum].append(runnum)
for s in subdirs.iterkeys():
for t in subdirs[s].iterkeys():
fname=mk_level2_fsf(taskid,s,t,subdirs[s][t],basedir,modelnum)
outfile.write('feat %s\n'%fname)
outfile.close()
print 'now launching using:'
print 'launch -s run_all_level2_%s.sh -n %sl2 -r 02:00:00'%(taskid,taskid)
launch_qsub.launch_qsub(script_name='run_all_level2_%s.sh'%taskid,runtime='02:00:00',jobname='%sl2'%taskid,email=False)
def main():
artimes=['08:00:00','12:00:00','24:00:00']
if len(sys.argv)>1:
dataset=sys.argv[1]
else:
usage()
if len(sys.argv)>2:
arlevel=int(sys.argv[2])
else:
arlevel=1
print 'assuming autorecon 1 (skullstrip)'
if len(sys.argv)>3:
basedir=sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
basedir='/corral-repl/utexas/poldracklab/openfmri/staged/'
if len(sys.argv)>4:
subdir=sys.argv[4]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
subdir='/corral-repl/utexas/poldracklab/openfmri/subdir/'
print 'assuming subdir: %s'%subdir
outfile=open('run_autorecon%d_%s.sh'%(arlevel,dataset),'w')
cmdctr=0
for d in os.listdir(os.path.join(basedir,dataset)):
if d[0:3]=='sub':
for m in os.listdir('%s/%s/anatomy/'%(os.path.join(basedir,dataset),d)):
if m=='highres001.nii.gz':
subnum=int(d.replace('sub',''))
outfile.write('recon-all -autorecon%d -subjid %s_sub%03d -sd %s\n'%(arlevel,dataset,subnum,subdir))
cmdctr+=1
outfile.close()
print 'now launch using:'
print 'launch -s run_autorecon%d_%s.sh -n %sar%d -r %s'%(arlevel,dataset,dataset,arlevel,artimes[arlevel-1])
launch_qsub.launch_qsub(script_name='run_autorecon%d_%s.sh'%(arlevel,dataset),runtime=artimes[arlevel-1],jobname='%sar%d'%(dataset,arlevel),email=False,parenv='1way',ncores=cmdctr*12)
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 = '/scratch/01329/poldrack/openfmri/staged/'
if len(sys.argv) > 3:
wait_process = int(sys.argv[3])
else:
wait_process = []
outfile = open('run_betfunc_%s.sh' % ds, 'w')
found_files = 0
dsdir = os.path.join(basedir, ds)
for d in glob.glob(os.path.join(dsdir, 'sub*/BOLD/*/bold.nii.gz')):
outfile.write('bet %s %s -F\n' % (d.replace(
'.nii', '_mcf.nii'), d.replace('.nii', '_mcf_brain.nii')))
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,
hold=wait_process)
else:
print 'no files found to process'
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 = "/scratch/01329/poldrack/openfmri/staged/"
outfile = open("run_betfunc_%s.sh" % ds, "w")
found_files = 0
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("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"
def main():
if len(sys.argv) > 2:
dataset = sys.argv[1]
modelnum = int(sys.argv[2])
else:
usage()
if len(sys.argv) > 3:
basedir = sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!' % basedir
sys.exit(1)
else:
basedir = os.path.abspath(os.curdir)
if not basedir[-1] == '/':
basedir = basedir + '/'
nonlinear = 1
if len(sys.argv) > 4:
nonlinear = int(sys.argv[4])
if nonlinear == 0:
print 'using linear registration'
outfile = open('mk_all_level1_%s.sh' % dataset, 'w')
smoothing = 0
if len(sys.argv) > 5:
smoothing = int(sys.argv[5])
tasknum_spec = 0
if len(sys.argv) > 6:
tasknum_spec = int(sys.argv[6])
use_inplane = 1
for d in os.listdir(basedir + dataset):
if d[0:3] == 'sub':
for bd in os.listdir('%s/%s/BOLD/' % (basedir + dataset, d)):
for m in os.listdir('%s/%s/BOLD/%s/' %
(basedir + dataset, d, bd)):
# TBD: add checking to handle case with no viable data
if m == 'bold_mcf_brain.nii.gz':
root = '%s/%s/BOLD/%s/' % (basedir + dataset, d, bd)
f_split = root.split('/')
scankey = '/' + '/'.join(
f_split[1:7]) + '/scan_key.txt'
taskid = f_split[6]
subnum = int(f_split[7].lstrip('sub'))
taskinfo = f_split[9].split('_')
tasknum = int(taskinfo[0].lstrip('task'))
if (tasknum_spec > 0) and not (tasknum
== tasknum_spec):
continue
runnum = int(taskinfo[1].lstrip('run'))
tr = float(load_scankey(scankey)['TR'])
# check for inplane
inplane = '/' + '/'.join(
f_split[1:8]) + '/anatomy/inplane001_brain.nii.gz'
if os.path.exists(inplane):
use_inplane = 1
else:
use_inplane = 0
print 'mk_level1_fsf("%s",%d,%d,%d,%d,%d,"%s",%d)' % (
taskid, subnum, tasknum, runnum, smoothing,
use_inplane, basedir, modelnum)
fname = mk_level1_fsf(taskid, subnum, tasknum, runnum,
smoothing, use_inplane, basedir,
nonlinear, modelnum)
outfile.write('feat %s\n' % fname)
outfile.close()
print 'now launching all feats:'
print "find %s/sub*/model/*.fsf |sed 's/^/feat /' > run_all_feats.sh; sh run_all_feats.sh" % taskid
f = open('mk_all_level1_%s.sh' % dataset)
l = f.readlines()
f.close()
njobs = len(l)
ncores = (njobs / 2) * 12
launch_qsub.launch_qsub(script_name='mk_all_level1_%s.sh' % dataset,
runtime='04:00:00',
jobname='%sl1' % dataset,
email=False,
parenv='2way',
ncores=ncores)
def main():
if len(sys.argv) > 2:
taskid = sys.argv[1]
modelnum = int(sys.argv[2])
else:
usage()
if len(sys.argv) > 3:
basedir = sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!' % basedir
sys.exit(1)
else:
basedir = os.path.abspath(os.curdir)
if len(sys.argv) > 4:
tasknum = int(sys.argv[4])
else:
tasknum = 0
if not basedir[-1] == '/':
basedir = basedir + '/'
if not os.path.exists(os.path.join(basedir, taskid, 'group')):
os.mkdir(os.path.join(basedir, taskid, 'group'))
if not os.path.exists(
os.path.join(basedir, taskid, 'group/model%03d' % modelnum)):
os.mkdir(os.path.join(basedir, taskid, 'group/model%03d' % modelnum))
featdirs = []
subdirs = {}
cond_key = load_condkey(basedir + taskid +
'/models/model%03d/condition_key.txt' % modelnum)
ntasks = len(cond_key)
print 'found %d tasks' % ntasks
fsfnames = []
if tasknum == 0:
tasks = range(1, ntasks + 1)
else:
tasks = [tasknum]
for t in tasks:
f = mk_level3_fsf(taskid, t, modelnum, basedir)
for i in f:
fsfnames.append(i)
outfile = open('run_all_level3_%s.sh' % taskid, 'w')
for f in fsfnames:
outfile.write('feat %s\n' % f)
outfile.close()
print 'now launching using:'
print 'launch -s run_all_level3_%s.sh -n %sl3 -r 01:00:00' % (taskid,
taskid)
launch_qsub.launch_qsub(script_name='run_all_level3_%s.sh' % taskid,
runtime='01:00:00',
jobname='%sl3' % taskid,
email=False)
def main():
if len(sys.argv) > 2:
taskid = sys.argv[1]
modelnum = int(sys.argv[2])
else:
usage()
if len(sys.argv) > 3:
basedir = sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!' % basedir
sys.exit(1)
else:
basedir = os.path.abspath(os.curdir)
if len(sys.argv) > 4:
task_spec = int(sys.argv[4])
print 'setting task spec to %d' % task_spec
else:
task_spec = 0
if not basedir[-1] == '/':
basedir = basedir + '/'
outfile = open('run_all_level2_%s.sh' % taskid, 'w')
featdirs = []
subdirs = {}
for d in os.listdir(basedir + taskid):
if d[0:3] == 'sub':
#print 'testing %s/%s/model/model%03d/'%(basedir+taskid,d,modelnum)
if os.path.exists('%s/%s/model/model%03d/' %
(basedir + taskid, d, modelnum)):
for m in os.listdir('%s/%s/model/model%03d/' %
(basedir + taskid, d, modelnum)):
if m[-5:] == '.feat':
featdirs.append(m)
fs = featdirs[-1]
print fs
subnum = int(d.replace('sub', ''))
if not subdirs.has_key(subnum):
subdirs[subnum] = {}
runnum = int(
fs.split('_')[1].split('.')[0].replace('run', ''))
tasknum = int(fs.split('_')[0].replace('task', ''))
if (task_spec > 0) and (not task_spec == tasknum):
print 'skipping tasknum %d (task_spec %d)' % (
tasknum, task_spec)
continue
if not subdirs[subnum].has_key(tasknum):
subdirs[subnum][tasknum] = []
subdirs[subnum][tasknum].append(runnum)
#print subdirs
for s in subdirs.iterkeys():
for t in subdirs[s].iterkeys():
#print 'testing %s/%s/sub%03d/model/model%03d/'%(basedir,taskid,s,modelnum)
if os.path.exists('%s/%s/sub%03d/model/model%03d/' %
(basedir, taskid, s, modelnum)):
fname = mk_level2_fsf(taskid, s, t, subdirs[s][t], basedir,
modelnum)
outfile.write('feat %s\n' % fname)
outfile.close()
print 'now launching using:'
print 'launch -s run_all_level2_%s.sh -n %sl2 -r 02:00:00' % (taskid,
taskid)
launch_qsub.launch_qsub(script_name='run_all_level2_%s.sh' % taskid,
runtime='02:00:00',
jobname='%sl2' % taskid,
email=False)
def main():
args = parse_command_line()
print args
smoothing = args.smoothing
use_inplane = args.use_inplane
basedir = os.path.abspath(args.basedir)
nonlinear = args.nonlinear
modelnum = args.modelnum
if not args.confound:
print 'omitting confound modeling'
dataset = args.taskid
if not args.test:
outfile = open('mk_all_level1_%s.sh' % dataset, 'w')
tasknum_spec = 'task*'
if not args.tasknum == None:
tasknum_spec = 'task%03d*' % args.tasknum
dsdir = os.path.join(basedir, dataset)
bolddirs = glob.glob(os.path.join(dsdir, 'sub*/BOLD/%s' % tasknum_spec))
print bolddirs
for root in bolddirs:
#print 'ROOT:',root
for m in glob.glob(os.path.join(root, 'bold_mcf_brain.nii.gz')):
#print 'BOLDFILE:',m
f_split = root.split('/')
#print f_split
scankey = '/' + '/'.join(f_split[1:7]) + '/scan_key.txt'
taskid = f_split[6]
subnum = int(f_split[7].lstrip('sub'))
taskinfo = f_split[9].split('_')
tasknum = int(taskinfo[0].lstrip('task'))
runnum = int(taskinfo[1].lstrip('run'))
#tr=float(load_scankey(scankey)['TR'])
# check for inplane
inplane = '/' + '/'.join(
f_split[1:8]) + '/anatomy/inplane001_brain.nii.gz'
## if args.nobbr:
## print 'using nobbr option'
## print 'mk_level1_fsf("%s",%d,%d,%d,%d,%d,"%s",%d)'%(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,modelnum)
## else:
## print 'mk_level1_fsf_bbr("%s",%d,%d,%d,%d,%d,"%s",%d)'%(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,modelnum)
if not args.test:
if args.nobbr:
fname = mk_level1_fsf(taskid, subnum, tasknum, runnum,
smoothing, use_inplane, basedir,
nonlinear, modelnum)
else:
fname = mk_level1_fsf_bbr(taskid, subnum, tasknum, runnum,
smoothing, use_inplane, basedir,
nonlinear, modelnum,
args.anatimg, args.confound,
args.hpf, args.whiten)
#print 'CMD: mk_level1_fsf_bbr(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,nonlinear,modelnum,args.anatimg,args.confound)'
outfile.write('feat %s\n' % fname)
if not args.test:
outfile.close()
if not args.test:
print 'now launching all feats:'
print "find %s/sub*/model/*.fsf |sed 's/^/feat /' > run_all_feats.sh; sh run_all_feats.sh" % args.taskid
f = open('mk_all_level1_%s.sh' % dataset)
l = f.readlines()
f.close()
njobs = len(l)
if args.parenv == '':
args.parenv = '6way'
way = float(args.parenv.replace('way', ''))
if args.ncores == 0:
ncores = (njobs / way) * 12.0
else:
ncores = args.ncores
if args.launch:
launch_qsub.launch_qsub(script_name='mk_all_level1_%s.sh' %
dataset,
runtime='04:00:00',
jobname='%sl1' % dataset,
email=False,
parenv=args.parenv,
ncores=ncores)
def main():
args=parse_command_line()
print args
smoothing=args.smoothing
use_inplane=args.use_inplane
basedir=os.path.abspath(args.basedir)
nonlinear=args.nonlinear
modelnum=args.modelnum
if not args.confound:
print 'omitting confound modeling'
dataset=args.taskid
if not args.test:
outfile=open('mk_all_level1_%s.sh'%dataset,'w')
tasknum_spec='task*'
if not args.tasknum==None:
tasknum_spec='task%03d*'%args.tasknum
dsdir=os.path.join(basedir,dataset)
bolddirs=glob.glob(os.path.join(dsdir,'sub*/BOLD/%s'%tasknum_spec))
print bolddirs
for root in bolddirs:
#print 'ROOT:',root
for m in glob.glob(os.path.join(root,'bold_mcf_brain.nii.gz')):
#print 'BOLDFILE:',m
f_split=root.split('/')
#print f_split
scankey='/'+'/'.join(f_split[1:7])+'/scan_key.txt'
taskid=f_split[6]
subnum=int(f_split[7].lstrip('sub'))
taskinfo=f_split[9].split('_')
tasknum=int(taskinfo[0].lstrip('task'))
runnum=int(taskinfo[1].lstrip('run'))
tr=float(load_scankey(scankey)['TR'])
# check for inplane
inplane='/'+'/'.join(f_split[1:8])+'/anatomy/inplane001_brain.nii.gz'
## if args.nobbr:
## print 'using nobbr option'
## print 'mk_level1_fsf("%s",%d,%d,%d,%d,%d,"%s",%d)'%(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,modelnum)
## else:
## print 'mk_level1_fsf_bbr("%s",%d,%d,%d,%d,%d,"%s",%d)'%(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,modelnum)
if not args.test:
if args.nobbr:
fname=mk_level1_fsf(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,nonlinear,modelnum)
else:
fname=mk_level1_fsf_bbr(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,nonlinear,modelnum,args.anatimg,args.confound,args.hpf,args.whiten)
#print 'CMD: mk_level1_fsf_bbr(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,nonlinear,modelnum,args.anatimg,args.confound)'
outfile.write('feat %s\n'%fname)
if not args.test:
outfile.close()
if not args.test:
print 'now launching all feats:'
print "find %s/sub*/model/*.fsf |sed 's/^/feat /' > run_all_feats.sh; sh run_all_feats.sh"%args.taskid
f=open('mk_all_level1_%s.sh'%dataset)
l=f.readlines()
f.close()
njobs=len(l)
if args.parenv=='':
args.parenv='6way'
way=float(args.parenv.replace('way',''))
if args.ncores==0:
ncores=(njobs/way)*12.0
else:
ncores=args.ncores
if args.launch:
launch_qsub.launch_qsub(script_name='mk_all_level1_%s.sh'%dataset,runtime='04:00:00',jobname='%sl1'%dataset,email=False,parenv=args.parenv,ncores=ncores)
def main():
if len(sys.argv)>2:
dataset=sys.argv[1]
modelnum=int(sys.argv[2])
else:
usage()
if len(sys.argv)>3:
basedir=sys.argv[3]
if not os.path.exists(basedir):
print 'basedir %s does not exist!'%basedir
sys.exit(1)
else:
basedir=os.path.abspath(os.curdir)
if not basedir[-1]=='/':
basedir=basedir+'/'
nonlinear=1
if len(sys.argv)>4:
nonlinear=int(sys.argv[4])
if nonlinear==0:
print 'using linear registration'
outfile=open('mk_all_level1_%s.sh'%dataset,'w')
smoothing=0
if len(sys.argv)>5:
smoothing=int(sys.argv[5])
tasknum_spec=0
if len(sys.argv)>6:
tasknum_spec=int(sys.argv[6])
use_inplane=1
for d in os.listdir(basedir+dataset):
if d[0:3]=='sub':
for bd in os.listdir('%s/%s/BOLD/'%(basedir+dataset,d)):
for m in os.listdir('%s/%s/BOLD/%s/'%(basedir+dataset,d,bd)):
# TBD: add checking to handle case with no viable data
if m=='bold_mcf_brain.nii.gz':
root='%s/%s/BOLD/%s/'%(basedir+dataset,d,bd)
f_split=root.split('/')
scankey='/'+'/'.join(f_split[1:7])+'/scan_key.txt'
taskid=f_split[6]
subnum=int(f_split[7].lstrip('sub'))
taskinfo=f_split[9].split('_')
tasknum=int(taskinfo[0].lstrip('task'))
if (tasknum_spec>0) and not (tasknum==tasknum_spec):
continue
runnum=int(taskinfo[1].lstrip('run'))
tr=float(load_scankey(scankey)['TR'])
# check for inplane
inplane='/'+'/'.join(f_split[1:8])+'/anatomy/inplane001_brain.nii.gz'
if os.path.exists(inplane):
use_inplane=1
else:
use_inplane=0
print 'mk_level1_fsf("%s",%d,%d,%d,%d,%d,"%s",%d)'%(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,modelnum)
fname=mk_level1_fsf(taskid,subnum,tasknum,runnum,smoothing,use_inplane,basedir,nonlinear,modelnum)
outfile.write('feat %s\n'%fname)
outfile.close()
print 'now launching all feats:'
print "find %s/sub*/model/*.fsf |sed 's/^/feat /' > run_all_feats.sh; sh run_all_feats.sh"%taskid
f=open('mk_all_level1_%s.sh'%dataset)
l=f.readlines()
f.close()
njobs=len(l)
ncores=(njobs/2)*12
launch_qsub.launch_qsub(script_name='mk_all_level1_%s.sh'%dataset,runtime='04:00:00',jobname='%sl1'%dataset,email=False,parenv='2way',ncores=ncores)
