def afni_copy(filename):
''' creates a ``+orig`` copy of the given dataset and returns the filename as a string '''
if nl.pkg_available('afni', True):
afni_filename = "%s+orig" % nl.prefix(filename)
if not os.path.exists(afni_filename + ".HEAD"):
nl.calc(filename, 'a', prefix=nl.prefix(filename))
return afni_filename
def afni_copy(filename):
''' creates a ``+orig`` copy of the given dataset and returns the filename as a string '''
if nl.pkg_available('afni',True):
afni_filename = "%s+orig" % nl.prefix(filename)
if not os.path.exists(afni_filename + ".HEAD"):
nl.calc(filename,'a',prefix=nl.prefix(filename))
return afni_filename
def skullstrip_template(dset, template, prefix=None, suffix=None, dilate=0):
'''Takes the raw anatomy ``dset``, aligns it to a template brain, and applies a templated skullstrip. Should produce fairly reliable skullstrips as long
as there is a decent amount of normal brain and the overall shape of the brain is normal-ish'''
if suffix == None:
suffix = '_sstemplate'
if prefix == None:
prefix = nl.suffix(dset, suffix)
if not os.path.exists(prefix):
with nl.notify('Running template-based skull-strip on %s' % dset):
dset = os.path.abspath(dset)
template = os.path.abspath(template)
tmp_dir = tempfile.mkdtemp()
cwd = os.getcwd()
with nl.run_in(tmp_dir):
nl.affine_align(template,
dset,
skull_strip=None,
cost='mi',
opts=['-nmatch', '100%'])
nl.run([
'3dQwarp', '-minpatch', '20', '-penfac', '10', '-noweight',
'-source',
nl.suffix(template, '_aff'), '-base', dset, '-prefix',
nl.suffix(template, '_qwarp')
],
products=nl.suffix(template, '_qwarp'))
info = nl.dset_info(nl.suffix(template, '_qwarp'))
max_value = info.subbricks[0]['max']
nl.calc([dset, nl.suffix(template, '_qwarp')],
'a*step(b-%f*0.05)' % max_value, prefix)
shutil.move(prefix, cwd)
shutil.rmtree(tmp_dir)
def qwarp_epi(dset, align_subbrick=5, suffix='_qwal', prefix=None):
'''aligns an EPI time-series using 3dQwarp
Very expensive and not efficient at all, but it can produce pretty impressive alignment for EPI time-series with significant
distortions due to motion'''
info = nl.dset_info(dset)
if info == None:
nl.notify('Error reading dataset "%s"' % (dset), level=nl.level.error)
return False
if prefix == None:
prefix = nl.suffix(dset, suffix)
dset_sub = lambda x: '_tmp_qwarp_epi-%s_%d.nii.gz' % (nl.prefix(dset), x)
try:
align_dset = nl.suffix(dset_sub(align_subbrick), '_warp')
nl.calc('%s[%d]' % (dset, align_subbrick),
expr='a',
prefix=align_dset,
datum='float')
for i in xrange(info.reps):
if i != align_subbrick:
nl.calc('%s[%d]' % (dset, i),
expr='a',
prefix=dset_sub(i),
datum='float')
nl.run([
'3dQwarp', '-nowarp', '-workhard', '-superhard',
'-minpatch', '9', '-blur', '0', '-pear', '-nopenalty',
'-base', align_dset, '-source',
dset_sub(i), '-prefix',
nl.suffix(dset_sub(i), '_warp')
],
quiet=True)
cmd = ['3dTcat', '-prefix', prefix]
if info.TR:
cmd += ['-tr', info.TR]
if info.slice_timing:
cmd += ['-tpattern', info.slice_timing]
cmd += [nl.suffix(dset_sub(i), '_warp') for i in xrange(info.reps)]
nl.run(cmd, quiet=True)
except Exception as e:
raise e
finally:
for i in xrange(info.reps):
for suffix in ['', 'warp']:
try:
os.remove(nl.suffix(dset_sub(i), suffix))
except:
pass
def roi_stats(mask,dset):
out_dict = {}
values = [{'Med': 'median', 'Min': 'min', 'Max': 'max',
'NZMean': 'nzmean', 'NZSum': 'nzsum', 'NZSigma': 'nzsigma',
'Mean': 'mean', 'Sigma': 'sigma', 'Mod': 'mode','NZcount':'nzvoxels'},
{'NZMod': 'nzmode', 'NZMed': 'nzmedian', 'NZMax': 'nzmax', 'NZMin': 'nzmin','Mean':'mean'}]
options = [['-nzmean','-nzsum','-nzvoxels','-minmax','-sigma','-nzsigma','-median','-mode'],
['-nzminmax','-nzmedian','-nzmode']]
if not nl.dset_grids_equal((mask,dset)):
i = nl.dset_info(dset)
grid_hash = '_' + '_'.join([str(x) for x in (i.voxel_size + i.voxel_dims)])
new_mask = nl.suffix(mask,grid_hash)
if not os.path.exists(new_mask):
nl.run(["3dfractionize","-template",dset,"-input",nl.calc(mask,"a",datum="short"),"-prefix",new_mask,"-preserve","-clip","0.2"])
mask = new_mask
for i in xrange(len(values)):
cmd = ['3dROIstats','-1Dformat','-nobriklab','-mask',mask] + options[i] + [dset]
out = subprocess.check_output(cmd).split('\n')
header = [(values[i][x.split('_')[0]],int(x.split('_')[1])) for x in out[1].split()[1:]]
for j in xrange(len(out)/2-1):
stats = [float(x) for x in out[(j+1)*2+1][1:].split()]
for s in xrange(len(stats)):
roi = header[s][1]
stat_name = header[s][0]
stat = stats[s]
if roi not in out_dict:
out_dict[roi] = {}
out_dict[roi][stat_name] = stat
return out_dict
def atlas_overlap(dset, atlas=None):
'''aligns ``dset`` to the TT_N27 atlas and returns ``(cost,overlap)``'''
atlas = find_atlas(atlas)
if atlas == None:
return None
cost_func = 'crM'
infile = os.path.abspath(dset)
tmpdir = tempfile.mkdtemp()
with nl.run_in(tmpdir):
o = nl.run([
'3dAllineate', '-verb', '-base', atlas, '-source', infile + '[0]',
'-NN', '-final', 'NN', '-cost', cost_func, '-nmatch', '20%',
'-onepass', '-fineblur', '2', '-cmass', '-prefix', 'test.nii.gz'
])
m = re.search(r'Final\s+cost = ([\d.]+) ;', o.output)
if m:
cost = float(m.group(1))
o = nl.run(['3dmaskave', '-mask', atlas, '-q', 'test.nii.gz'],
stderr=None)
data_thresh = float(o.output) / 4
i = nl.dset_info('test.nii.gz')
o = nl.run([
'3dmaskave', '-q', '-mask', 'SELF', '-sum',
nl.calc([atlas, 'test.nii.gz'],
'equals(step(a-10),step(b-%.2f))' % data_thresh)
],
stderr=None)
overlap = 100 * float(
o.output) / (i.voxel_dims[0] * i.voxel_dims[1] * i.voxel_dims[2])
try:
shutil.rmtree(tmpdir)
except:
pass
return (cost, overlap)
def qwarp_epi(dset,align_subbrick=5,suffix='_qwal',prefix=None):
'''aligns an EPI time-series using 3dQwarp
Very expensive and not efficient at all, but it can produce pretty impressive alignment for EPI time-series with significant
distortions due to motion'''
info = nl.dset_info(dset)
if info==None:
nl.notify('Error reading dataset "%s"' % (dset),level=nl.level.error)
return False
if prefix==None:
prefix = nl.suffix(dset,suffix)
dset_sub = lambda x: '_tmp_qwarp_epi-%s_%d.nii.gz' % (nl.prefix(dset),x)
try:
align_dset = nl.suffix(dset_sub(align_subbrick),'_warp')
nl.calc('%s[%d]' % (dset,align_subbrick),expr='a',prefix=align_dset,datum='float')
for i in xrange(info.reps):
if i != align_subbrick:
nl.calc('%s[%d]' % (dset,i),expr='a',prefix=dset_sub(i),datum='float')
nl.run([
'3dQwarp', '-nowarp',
'-workhard', '-superhard', '-minpatch', '9', '-blur', '0',
'-pear', '-nopenalty',
'-base', align_dset,
'-source', dset_sub(i),
'-prefix', nl.suffix(dset_sub(i),'_warp')
],quiet=True)
cmd = ['3dTcat','-prefix',prefix]
if info.TR:
cmd += ['-tr',info.TR]
if info.slice_timing:
cmd += ['-tpattern',info.slice_timing]
cmd += [nl.suffix(dset_sub(i),'_warp') for i in xrange(info.reps)]
nl.run(cmd,quiet=True)
except Exception as e:
raise e
finally:
for i in xrange(info.reps):
for suffix in ['','warp']:
try:
os.remove(nl.suffix(dset_sub(i),suffix))
except:
pass
def temporal_snr(signal_dset,
noise_dset,
mask=None,
prefix='temporal_snr.nii.gz'):
'''Calculates temporal SNR by dividing average signal of ``signal_dset`` by SD of ``noise_dset``.
``signal_dset`` should be a dataset that contains the average signal value (i.e., nothing that has
been detrended by removing the mean), and ``noise_dset`` should be a dataset that has all possible
known signal fluctuations (e.g., task-related effects) removed from it (the residual dataset from a
deconvolve works well)'''
for d in [('mean', signal_dset), ('stdev', noise_dset)]:
new_d = nl.suffix(d[1], '_%s' % d[0])
cmd = ['3dTstat', '-%s' % d[0], '-prefix', new_d]
if mask:
cmd += ['-mask', mask]
cmd += [d[1]]
nl.run(cmd, products=new_d)
nl.calc([nl.suffix(signal_dset, '_mean'),
nl.suffix(noise_dset, '_stdev')],
'a/b',
prefix=prefix)
def voxel_count(dset, p=None, positive_only=False, mask=None, ROI=None):
''' returns the number of non-zero voxels
:p: threshold the dataset at the given *p*-value, then count
:positive_only: only count positive values
:mask: count within the given mask
:ROI: only use the ROI with the given value (or list of values) within the mask
if ROI is 'all' then return the voxel count of each ROI
as a dictionary
'''
if p:
dset = nl.thresh(dset, p, positive_only)
else:
if positive_only:
dset = nl.calc(dset, 'step(a)')
count = 0
devnull = open(os.devnull, "w")
if mask:
cmd = [
'3dROIstats', '-1Dformat', '-nomeanout', '-nobriklab', '-nzvoxels'
]
cmd += ['-mask', str(mask), str(dset)]
out = subprocess.check_output(cmd, stderr=devnull).split('\n')
if len(out) < 4:
return 0
rois = [
int(x.replace('NZcount_', '')) for x in out[1].strip()[1:].split()
]
counts = [
int(x.replace('NZcount_', '')) for x in out[3].strip().split()
]
count_dict = None
if ROI == None:
ROI = rois
if ROI == 'all':
count_dict = {}
ROI = rois
else:
if not isinstance(ROI, list):
ROI = [ROI]
for r in ROI:
if r in rois:
roi_count = counts[rois.index(r)]
if count_dict != None:
count_dict[r] = roi_count
else:
count += roi_count
else:
cmd = ['3dBrickStat', '-slow', '-count', '-non-zero', str(dset)]
count = int(subprocess.check_output(cmd, stderr=devnull).strip())
if count_dict:
return count_dict
return count
def skullstrip_template(dset,template,prefix=None,suffix=None,dilate=0):
'''Takes the raw anatomy ``dset``, aligns it to a template brain, and applies a templated skullstrip. Should produce fairly reliable skullstrips as long
as there is a decent amount of normal brain and the overall shape of the brain is normal-ish'''
if suffix==None:
suffix = '_sstemplate'
if prefix==None:
prefix = nl.suffix(dset,suffix)
if not os.path.exists(prefix):
with nl.notify('Running template-based skull-strip on %s' % dset):
dset = os.path.abspath(dset)
template = os.path.abspath(template)
tmp_dir = tempfile.mkdtemp()
cwd = os.getcwd()
with nl.run_in(tmp_dir):
nl.affine_align(template,dset,skull_strip=None,cost='mi',opts=['-nmatch','100%'])
nl.run(['3dQwarp','-minpatch','20','-penfac','10','-noweight','-source',nl.suffix(template,'_aff'),'-base',dset,'-prefix',nl.suffix(template,'_qwarp')],products=nl.suffix(template,'_qwarp'))
info = nl.dset_info(nl.suffix(template,'_qwarp'))
max_value = info.subbricks[0]['max']
nl.calc([dset,nl.suffix(template,'_qwarp')],'a*step(b-%f*0.05)'%max_value,prefix)
shutil.move(prefix,cwd)
shutil.rmtree(tmp_dir)
def roi_stats(mask, dset):
out_dict = {}
values = [{
'Med': 'median',
'Min': 'min',
'Max': 'max',
'NZMean': 'nzmean',
'NZSum': 'nzsum',
'NZSigma': 'nzsigma',
'Mean': 'mean',
'Sigma': 'sigma',
'Mod': 'mode',
'NZcount': 'nzvoxels'
}, {
'NZMod': 'nzmode',
'NZMed': 'nzmedian',
'NZMax': 'nzmax',
'NZMin': 'nzmin',
'Mean': 'mean'
}]
options = [[
'-nzmean', '-nzsum', '-nzvoxels', '-minmax', '-sigma', '-nzsigma',
'-median', '-mode'
], ['-nzminmax', '-nzmedian', '-nzmode']]
if not nl.dset_grids_equal((mask, dset)):
i = nl.dset_info(dset)
grid_hash = '_' + '_'.join(
[str(x) for x in (i.voxel_size + i.voxel_dims)])
new_mask = nl.suffix(mask, grid_hash)
if not os.path.exists(new_mask):
nl.run([
"3dfractionize", "-template", dset, "-input",
nl.calc(mask, "a", datum="short"), "-prefix", new_mask,
"-preserve", "-clip", "0.2"
])
mask = new_mask
for i in xrange(len(values)):
cmd = ['3dROIstats', '-1Dformat', '-nobriklab', '-mask', mask
] + options[i] + [dset]
out = subprocess.check_output(cmd).split('\n')
header = [(values[i][x.split('_')[0]], int(x.split('_')[1]))
for x in out[1].split()[1:]]
for j in xrange(len(out) / 2 - 1):
stats = [float(x) for x in out[(j + 1) * 2 + 1][1:].split()]
for s in xrange(len(stats)):
roi = header[s][1]
stat_name = header[s][0]
stat = stats[s]
if roi not in out_dict:
out_dict[roi] = {}
out_dict[roi][stat_name] = stat
return out_dict
def voxel_count(dset,p=None,positive_only=False,mask=None,ROI=None):
''' returns the number of non-zero voxels
:p: threshold the dataset at the given *p*-value, then count
:positive_only: only count positive values
:mask: count within the given mask
:ROI: only use the ROI with the given value (or list of values) within the mask
if ROI is 'all' then return the voxel count of each ROI
as a dictionary
'''
if p:
dset = nl.thresh(dset,p,positive_only)
else:
if positive_only:
dset = nl.calc(dset,'step(a)')
count = 0
devnull = open(os.devnull,"w")
if mask:
cmd = ['3dROIstats','-1Dformat','-nomeanout','-nobriklab', '-nzvoxels']
cmd += ['-mask',str(mask),str(dset)]
out = subprocess.check_output(cmd,stderr=devnull).split('\n')
if len(out)<4:
return 0
rois = [int(x.replace('NZcount_','')) for x in out[1].strip()[1:].split()]
counts = [int(x.replace('NZcount_','')) for x in out[3].strip().split()]
count_dict = None
if ROI==None:
ROI = rois
if ROI=='all':
count_dict = {}
ROI = rois
else:
if not isinstance(ROI,list):
ROI = [ROI]
for r in ROI:
if r in rois:
roi_count = counts[rois.index(r)]
if count_dict!=None:
count_dict[r] = roi_count
else:
count += roi_count
else:
cmd = ['3dBrickStat', '-slow', '-count', '-non-zero', str(dset)]
count = int(subprocess.check_output(cmd,stderr=devnull).strip())
if count_dict:
return count_dict
return count
def inside_brain(stat_dset, atlas=None, p=0.001):
'''calculates the percentage of voxels above a statistical threshold inside a brain mask vs. outside it
if ``atlas`` is ``None``, it will try to find ``TT_N27``'''
atlas = find_atlas(atlas)
if atlas == None:
return None
mask_dset = nl.suffix(stat_dset, '_atlasfrac')
nl.run([
'3dfractionize', '-template',
nl.strip_subbrick(stat_dset), '-input',
nl.calc([atlas], '1+step(a-100)', datum='short'), '-preserve', '-clip',
'0.2', '-prefix', mask_dset
],
products=mask_dset,
quiet=True,
stderr=None)
s = nl.roi_stats(mask_dset, nl.thresh(stat_dset, p))
return 100.0 * s[2]['nzvoxels'] / (s[1]['nzvoxels'] + s[2]['nzvoxels'])
def skull_strip(dset, suffix='_ns', prefix=None, unifize=True):
''' use bet to strip skull from given anatomy '''
# should add options to use betsurf and T1/T2 in the future
# Since BET fails on weirdly distributed datasets, I added 3dUnifize in... I realize this makes this dependent on AFNI. Sorry, :)
if prefix == None:
prefix = nl.suffix(dset, suffix)
unifize_dset = nl.suffix(dset, '_u')
cmd = bet2 if bet2 else 'bet2'
if unifize:
info = nl.dset_info(dset)
if info == None:
nl.notify('Error: could not read info for dset %s' % dset,
level=nl.level.error)
return False
cmd = os.path.join(fsl_dir, cmd) if fsl_dir else cmd
cutoff_value = nl.max(dset) * 0.05
nl.run([
'3dUnifize', '-prefix', unifize_dset,
nl.calc(dset, 'step(a-%f)*a' % cutoff_value)
],
products=unifize_dset)
else:
unifize_dset = dset
nl.run([cmd, unifize_dset, prefix, '-w', 0.5], products=prefix)