def do_bet(head, fracval, fourD, logpath, tmpdir, prov_list):
bet = fsl.BET()
prefile = head.split("/")[-1]
prefile_wo_ext = prefile[: prefile.find(".nii")]
if fourD == False:
bet.inputs.in_file = head
bet.inputs.out_file = tmpdir + prefile_wo_ext + version + str(fracval) + "frac_3D.nii.gz"
bet.inputs.frac = fracval
bet.inputs.mask = True
xnatmaster.add_to_log(logpath, bet.cmdline)
prov_list = xnatmaster.track_provenance(
prov_list,
"/import/monstrum/Applications/fsl_4.1.7/bin/bet",
"v2",
head + " " + tmpdir + prefile_wo_ext + version + str(fracval) + "frac_3D.nii.gz -m",
)
result = bet.run()
slice_bet(tmpdir, tmpdir + prefile_wo_ext + version + str(fracval) + "frac_3D.nii.gz")
return tmpdir + prefile_wo_ext + version + str(fracval) + "frac_3D"
else:
bet.inputs.in_file = head
bet.inputs.mask = True
bet.inputs.out_file = tmpdir + prefile_wo_ext + version + str(fracval) + "frac_4D.nii.gz"
bet.inputs.functional = True
bet.inputs.frac = fracval
xnatmaster.add_to_log(logpath, bet.cmdline)
prov_list = xnatmaster.track_provenance(
prov_list,
"/import/monstrum/Applications/fsl_4.1.7/bin/bet",
"v2",
head + " " + tmpdir + prefile_wo_ext + version + str(fracval) + "frac_4D.nii.gz -F",
)
result = bet.run()
slice_bet(tmpdir, tmpdir + prefile_wo_ext + version + str(fracval) + "frac_4D.nii.gz")
return tmpdir + prefile_wo_ext + version + str(fracval) + "frac_4D"
def do_bet(head, fracval, fourD, logpath, tmpdir, prov_list):
bet = fsl.BET()
prefile = head.split('/')[-1]
prefile_wo_ext = prefile[:prefile.find(".nii")]
if fourD == False:
bet.inputs.in_file = head
bet.inputs.out_file = tmpdir + prefile_wo_ext + version + str(
fracval) + 'frac_3D.nii.gz'
bet.inputs.frac = fracval
bet.inputs.mask = True
xnatmaster.add_to_log(logpath, bet.cmdline)
prov_list = xnatmaster.track_provenance(
prov_list, '/import/monstrum/Applications/fsl_4.1.7/bin/bet', 'v2',
head + ' ' + tmpdir + prefile_wo_ext + version + str(fracval) +
'frac_3D.nii.gz -m')
result = bet.run()
slice_bet(
tmpdir, tmpdir + prefile_wo_ext + version + str(fracval) +
'frac_3D.nii.gz')
return tmpdir + prefile_wo_ext + version + str(fracval) + 'frac_3D'
else:
bet.inputs.in_file = head
bet.inputs.mask = True
bet.inputs.out_file = tmpdir + prefile_wo_ext + version + str(
fracval) + 'frac_4D.nii.gz'
bet.inputs.functional = True
bet.inputs.frac = fracval
xnatmaster.add_to_log(logpath, bet.cmdline)
prov_list = xnatmaster.track_provenance(
prov_list, '/import/monstrum/Applications/fsl_4.1.7/bin/bet', 'v2',
head + ' ' + tmpdir + prefile_wo_ext + version + str(fracval) +
'frac_4D.nii.gz -F')
result = bet.run()
slice_bet(
tmpdir, tmpdir + prefile_wo_ext + version + str(fracval) +
'frac_4D.nii.gz')
return tmpdir + prefile_wo_ext + version + str(fracval) + 'frac_4D'
formname = formname.replace(" ", "_")
nonzeroi = str(i).lstrip("0")
nonzerosubid = str(subj_id).lstrip("0")
newoutdir = (
outdir + str(nonzerosubid) + "_" + str(nonzeroi) + "/" + str(seq_id) + "_" + str(seqname) + "/bet/"
)
if (
not xnatmaster.ensure_dir_exists(newoutdir)
and xnatmaster.ensure_write_permissions(newoutdir)
and not xnatmaster.ensure_dir_exists(newtmpdir)
and xnatmaster.ensure_write_permissions(newtmpdir)
):
sys.exit(1)
##New dir str end
print "Form: " + str(formname)
xnatmaster.add_to_log(logpath, "Processing sequence: " + seqname + ":" + str(seq_id))
global prov_list
prov_list = []
betfound = 0
niftifound = 0
donewithsequence = 0
niftifound = xnatmaster.existing_nifti(i, seq_id, central)
if niftifound < 1:
print "Could not find nifti for this scan. Please run dicoms2nifti before this script."
sys.exit(1)
if findexisting == "1":
xnatmaster.add_to_log(logpath, "Checking for existing BET: " + seq_id)
betfound = xnatmaster.existing_bet(i, seq_id, central)
if betfound > 0:
if download == "1":
xnatmaster.get_bet(i, seq_id, newoutdir, central, proj_name, subj_id)
formname = formname.replace("(", "_")
formname = formname.replace(")", "_")
formname = formname.replace(" ", "_")
nonzeroi = str(i).lstrip('0')
nonzerosubid = str(subj_id).lstrip('0')
newoutdir = outdir + str(nonzerosubid) + '_' + str(
nonzeroi) + '/' + str(seq_id) + '_' + str(seqname) + '/bet/'
if not xnatmaster.ensure_dir_exists(
newoutdir) and xnatmaster.ensure_write_permissions(
newoutdir) and not xnatmaster.ensure_dir_exists(
newtmpdir) and xnatmaster.ensure_write_permissions(
newtmpdir):
sys.exit(1)
##New dir str end
print "Form: " + str(formname)
xnatmaster.add_to_log(
logpath, "Processing sequence: " + seqname + ":" + str(seq_id))
global prov_list
prov_list = []
betfound = 0
niftifound = 0
donewithsequence = 0
niftifound = xnatmaster.existing_nifti(i, seq_id, central)
if niftifound < 1:
print "Could not find nifti for this scan. Please run dicoms2nifti before this script."
sys.exit(1)
if findexisting == '1':
xnatmaster.add_to_log(logpath,
"Checking for existing BET: " + seq_id)
betfound = xnatmaster.existing_bet(i, seq_id, central)
if betfound > 0:
if download == '1':
