def run_toafni(config, env):
'''convert surfaces to AFNI (or SUMA, rather) format'''
cmds = []
sd = config['sumadir']
sid = config['sid']
if sid is None:
raise ValueError("Subject id is not set, cannot continue")
fs_sid = config['fs_sid']
# files that should exist if Make_Spec_FS was run successfully
checkfns = ['brainmask.nii', 'T1.nii', 'aseg.nii']
filesexist = all([os.path.exists('%s/%s' % (sd, fn)) for fn in checkfns])
if config['overwrite'] or not filesexist:
if config['overwrite']:
if filesexist:
cmds.append('rm -rf "%s"' % sd)
cmds.append('cd %(surfdir)s;@SUMA_Make_Spec_FS -sid %(sid)s -no_ld' %
config)
utils.run_cmds(cmds, env)
else:
print "SUMA conversion appears to have been performed already for %s in %s" % (
sid, sd)
def run_toafni(config, env):
'''convert surfaces to AFNI (or SUMA, rather) format'''
cmds = []
sd = config['sumadir']
sid = config['sid']
if sid is None:
raise ValueError("Subject id is not set, cannot continue")
fs_sid = config['fs_sid']
# files that should exist if Make_Spec_FS was run successfully
checkfns = ['brainmask.nii',
'T1.nii',
'aseg.nii']
filesexist = all([os.path.exists('%s/%s' % (sd, fn)) for fn in checkfns])
if config['overwrite'] or not filesexist:
if config['overwrite']:
if filesexist:
cmds.append('rm -rf "%s"' % sd)
cmds.append('cd %(surfdir)s;@SUMA_Make_Spec_FS -sid %(sid)s -no_ld' % config)
utils.run_cmds(cmds, env)
else:
print "SUMA conversion appears to have been performed already for %s in %s" % (sid, sd)
def run_mapico(config, env):
'''run MapIcosehedron to convert surfaces to standard topology'''
sumadir = config['sumadir']
firstcmd = 'cd "%s" || exit 1' % sumadir
cmds = []
icolds, hemis = _get_hemis_icolds(config)
sid = config['sid'] # subject id
ext = '.asc' # input is always ascii
for icold in icolds:
icoprefix = config['mi_icopat'] % icold
spherefns = []
for hemi in hemis:
if not config['overwrite']:
# the last file that is generated by MapIcosahedron
lastsurffn = '%s/%s%sh.sphere.reg%s' % (
sumadir, config['mi_icopat'] % icold, hemi, ext)
spherefns.append(lastsurffn)
if os.path.exists(lastsurffn):
print(
"Seems MapIcosahedron was already run for %sh with ld=%d"
% (hemi, icold))
continue
cmd = (
'MapIcosahedron -overwrite -spec %s_%sh.spec -ld %d -fix_cut_surfaces -prefix %s'
% (sid, hemi, icold, icoprefix))
cmds.append(cmd)
if cmds:
cmd = '%s;%s' % (firstcmd, ';'.join(cmds))
utils.run_cmds(cmd, env)
cmds = []
if len(spherefns) == 2 and 'l' in hemis and 'r' in hemis:
spheres = map(surf.read, spherefns)
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
mappathfn = os.path.join(sumadir, mapfn)
if config['overwrite'] or not os.path.exists(mappathfn):
eps = .001
print "Computing bijection between nodes (ico=%d) - this may take a while" % icold
bijection = surf.get_sphere_left_right_mapping(
spheres[0], spheres[1], eps)
with open(mappathfn, 'w') as f:
f.write('\n'.join(map(str, bijection)))
print "Written bijection to %s" % mappathfn
def run_mapico(config, env):
"""run MapIcosehedron to convert surfaces to standard topology"""
sumadir = config["sumadir"]
firstcmd = 'cd "%s" || exit 1' % sumadir
cmds = []
icolds, hemis = _get_hemis_icolds(config)
sid = config["sid"] # subject id
ext = ".asc" # input is always ascii
for icold in icolds:
icoprefix = config["mi_icopat"] % icold
spherefns = []
for hemi in hemis:
if not config["overwrite"]:
# the last file that is generated by MapIcosahedron
lastsurffn = "%s/%s%sh.sphere.reg%s" % (sumadir, config["mi_icopat"] % icold, hemi, ext)
spherefns.append(lastsurffn)
if os.path.exists(lastsurffn):
print ("Seems MapIcosahedron was already run for %sh with ld=%d" % (hemi, icold))
continue
cmd = "MapIcosahedron -overwrite -spec %s_%sh.spec -ld %d -fix_cut_surfaces -prefix %s" % (
sid,
hemi,
icold,
icoprefix,
)
cmds.append(cmd)
if cmds:
cmd = "%s;%s" % (firstcmd, ";".join(cmds))
utils.run_cmds(cmd, env)
cmds = []
if len(spherefns) == 2 and "l" in hemis and "r" in hemis:
spheres = map(surf.read, spherefns)
mapfn = (config["mi_icopat"] % icold) + config["hemimappingsuffix"]
mappathfn = pathjoin(sumadir, mapfn)
if config["overwrite"] or not os.path.exists(mappathfn):
eps = 0.001
print "Computing bijection between nodes (ico=%d) - this may take a while" % icold
bijection = surf.get_sphere_left_right_mapping(spheres[0], spheres[1], eps)
with open(mappathfn, "w") as f:
f.write("\n".join(map(str, bijection)))
print "Written bijection to %s" % mappathfn
def run_mapico(config, env):
'''run MapIcosehedron to convert surfaces to standard topology'''
sumadir = config['sumadir']
firstcmd = 'cd "%s" || exit 1' % sumadir
cmds = []
icolds, hemis = _get_hemis_icolds(config)
sid = config['sid'] # subject id
for icold in icolds:
icoprefix = config['mi_icopat'] % icold
spherefns = []
for hemi in hemis:
if not config['overwrite']:
# the last file that is generated by MapIcosahedron
lastsurffn = '%s/%s%sh.sphere.reg.asc' % (sumadir, config['mi_icopat'] % icold, hemi)
spherefns.append(lastsurffn)
if os.path.exists(lastsurffn):
print("Seems MapIcosahedron was already run for %sh with ld=%d" % (hemi, icold))
continue
cmd = ('MapIcosahedron -overwrite -spec %s_%sh.spec -ld %d -prefix %s' %
(sid, hemi, icold, icoprefix))
cmds.append(cmd)
if cmds:
cmd = '%s;%s' % (firstcmd, ';'.join(cmds))
utils.run_cmds(cmd, env)
cmds = []
if len(spherefns) == 2 and 'l' in hemis and 'r' in hemis:
spheres = map(surf.read, spherefns)
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
mappathfn = os.path.join(sumadir, mapfn)
if config['overwrite'] or not os.path.exists(mappathfn):
eps = .001
print "Computing bijection between nodes (ico=%d) - this may take a while" % icold
bijection = surf_fs_asc.sphere_reg_leftrightmapping(spheres[0],
spheres[1],
eps)
with open(mappathfn, 'w') as f:
f.write('\n'.join(map(str, bijection)))
print "Written bijection to %s" % mappathfn
def compute_fwhm(config):
# helper function - called by critical_clustersize
# computes FWHM of residuals of input data and stores in config
output_dir = c['output_dir']
is_surf = _is_surf(config)
ext, ext1D = _ext(config), _ext(config, for1D=True)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
cmds = ['cd "%s"' % output_dir]
# if surfaces and needs padding, do that first
pad_to_node = config['pad_to_node']
if is_surf and pad_to_node:
data_files = []
for i, fn in enumerate(c['data_files']):
fn_pad = 'pad_%d%s' % (i, ext)
cmds.append("; ConvertDset -overwrite -pad_to_node %d -input %s'[%d]' -prefix ./%s" %
(pad_to_node, fn, config['brik_index'], fn_pad))
data_files.append(fn_pad)
pad_files = data_files
brik_index = 0
else:
data_files = c['data_files']
pad_files = []
brik_index = c['brik_index']
# bucket data from all participants into a single file
buck_fn = _fn(config, 'buck')
cmds.append('; 3dbucket -overwrite -prefix %s' % buck_fn)
for fn in data_files:
cmds.append(" %s'[%d]'" % (fn, brik_index))
# also store as 1D (won't hurt)
if is_surf:
buck_fn_1D = _fn(config, 'buck', ext1D)
cmds.append('; ConvertDset -overwrite -o_1D -prefix %s -input %s' %
(buck_fn_1D, buck_fn))
else:
buck_fn_1D = buck_fn
# compute group mean
mean_fn = _fn(config, 'mean')
cmds.append('; 3dTstat -overwrite -prefix %s %s' % (mean_fn, buck_fn))
# compute residuals, and estimate FWHM for each of them
# store FWHM output in fwhm_fn
fwhm_fn = pathjoin(output_dir, _fn(config, 'fwhm', '.1D'))
cmds.append('; echo > "%s"' % fwhm_fn)
resid_fns = []
for i in xrange(len(c['data_files'])):
fn = _fn(config, 'resid_%d' % i)
cmds.append("; 3dcalc -overwrite -prefix %s -a %s -b %s'[%d]' -expr 'a-b'"
% (fn, mean_fn, buck_fn, i))
msk = _mask_expr(config)
if is_surf:
surf_fn = c['surface_file']
cmds.append("; SurfFWHM %s -input %s -i_fs %s"
"| grep ^FWHM | cut -f2 -d'=' >> '%s'" %
(msk, fn, surf_fn, fwhm_fn))
else:
cmds.append('; 3dFWHMx %s %s | cut -c18- >> %s' % (msk, fn, fwhm_fn))
resid_fns.append(fn)
cmd = ''.join(cmds)
utils.run_cmds(cmd)
# read FWHM values and store in config
with open(fwhm_fn) as f:
fwhms = f.read().split()
print fwhms
print fwhm_fn
config['all_fwhms'] = fwhms # all FWHMs (for each participant)
config['fwhm'] = sum(map(float, fwhms)) / len(fwhms) # average FWHM
config['buck_fn'] = buck_fn
config['buck_fn_1D'] = buck_fn_1D
mean_fwhm_fn = pathjoin(output_dir, _fn(config, 'mean_fwhm', '.1D'))
with open(mean_fwhm_fn, 'w') as f:
f.write('%.3f\n' % config['fwhm'])
tmpfns = resid_fns + pad_files + [mean_fn]
print "TEMP"
print tmpfns
_remove_files(config, tmpfns)
def apply_clustersize(config):
# applies the critical cluster size to the original data
#
# assumes that critical_clustersize(config) has been run
output_dir = config['output_dir']
pthr = config['pthr']
tthr = config['tthr']
niter = config['niter']
buck_fn_1D = config['buck_fn_1D']
is_surf = _is_surf(config)
if is_surf:
surf_fn = config['surface_file']
cmds = ['cd "%s"' % output_dir]
# run ttest on original data
infix = 'ttest_t%(tthr)s' % config
ttest_fn = _fn(config, infix)
msk = _mask_expr(config)
# NOTE: for surfaces, apply mask below (SurfClust)
# but in volumes, apply it here
if is_surf:
cmds.append('; 3dttest++ -ok_1D_text -overwrite -prefix %s -setA %s' % (ttest_fn, buck_fn_1D))
else:
cmds.append('; 3dttest++ %s -overwrite -prefix %s -setA %s' % (msk, ttest_fn, buck_fn_1D))
# sort cluster sizes
clsize = list(config['max_size'])
clsize.sort()
# get critical cluster size
idx = _critical_size_index(config)
critical_size = clsize[idx]
print "critical size %s (p=%s)" % (critical_size, pthr)
# apply critical size to t-test of original data
infix += '_clustp%s_%dit' % (pthr, niter)
if not is_surf:
# for surfaces the size is included in the filename automatically
infix += '_%svx' % critical_size
# set file names
dset_out = _fn(config, infix)
log_out = _fn(config, infix, '.txt')
if is_surf:
cmds.append('; SurfClust %s -i_fs %s -input %s 1 -rmm -1 '
' -thresh %f -thresh_col 1 -amm2 %f -out_clusterdset -prefix %s > %s' %
(msk, surf_fn, ttest_fn, tthr, critical_size, dset_out, log_out))
else:
dset_out_msk = _fn(config, infix + '_msk')
cmds.append("; 3dclust -overwrite -1noneg -1clip %f "
" -prefix %s -savemask %s 0 -%f %s'[1]' > %s" %
(tthr, dset_out, dset_out_msk, critical_size, ttest_fn, log_out))
cmd = "".join(cmds)
utils.run_cmds(cmd)
def run_skullstrip(config, env):
if config['identity']:
return
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn)
for fn in ['brain.nii',
'T1.nii']]
surfvol_trgs = ['%s/%s' % (refdir, fn)
for fn in ['%s_SurfVol_ss+orig.HEAD' % sid,
'%s_SurfVol+orig.HEAD' % sid]]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dcopy -overwrite %s ./%s' %
(refdir, src, trg_short))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
if 'nii' in e_e:
# ensure e_n+orig is in refdir
if overwrite or not utils.afni_fileexists('%s/%s+orig.HEAD' % (refdir, e_n)):
print "Converting %s from NIFTI to AFNI format" % e_n
cmds.append('cd "%s"; 3dbucket -overwrite -prefix ./%s+orig %s' % (refdir, e_n, expvol_src))
cmds.append('if [ -e %s/%s+tlrc.HEAD ]; then 3drefit -view orig -space ORIG %s/%s+tlrc; else echo "File in orig orientation - no refit necessary"; fi' % (refdir, e_n, refdir, e_n))
expvol_src = '%s/%s+orig.HEAD' % (refdir, e_n)
expvol_trg = '%s/%s+orig.HEAD' % (refdir, expvol_trg_prefix)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append('cd "%s";3dSkullStrip -overwrite -prefix ./%s+orig -input %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
print "No skull strip because already exists: %s+orig" % expvol_trg_prefix
utils.run_cmds(cmds, env)
def apply_clustersize(config):
# applies the critical cluster size to the original data
#
# assumes that critical_clustersize(config) has been run
output_dir = config['output_dir']
pthr = config['pthr']
tthr = config['tthr']
niter = config['niter']
buck_fn_1D = config['buck_fn_1D']
is_surf = _is_surf(config)
if is_surf:
surf_fn = config['surface_file']
cmds = ['cd "%s"' % output_dir]
# run ttest on original data
infix = 'ttest_t%(tthr)s' % config
ttest_fn = _fn(config, infix)
msk = _mask_expr(config)
# NOTE: for surfaces, apply mask below (SurfClust)
# but in volumes, apply it here
if is_surf:
cmds.append('; 3dttest++ -ok_1D_text -overwrite -prefix %s -setA %s' % (ttest_fn, buck_fn_1D))
else:
cmds.append('; 3dttest++ %s -overwrite -prefix %s -setA %s' % (msk, ttest_fn, buck_fn_1D))
# sort cluster sizes
clsize = list(config['max_size'])
clsize.sort()
# get critical cluster size
idx = _critical_size_index(config)
critical_size = clsize[idx]
print("critical size %s (p=%s)" % (critical_size, pthr))
# apply critical size to t-test of original data
infix += '_clustp%s_%dit' % (pthr, niter)
if not is_surf:
# for surfaces the size is included in the filename automatically
infix += '_%svx' % critical_size
# set file names
dset_out = _fn(config, infix)
log_out = _fn(config, infix, '.txt')
if is_surf:
cmds.append('; SurfClust %s -i_fs %s -input %s 1 -rmm -1 '
' -thresh %f -thresh_col 1 -amm2 %f -out_clusterdset -prefix %s > %s' %
(msk, surf_fn, ttest_fn, tthr, critical_size, dset_out, log_out))
else:
dset_out_msk = _fn(config, infix + '_msk')
cmds.append("; 3dclust -overwrite -1noneg -1clip %f "
" -prefix %s -savemask %s 0 -%f %s'[1]' > %s" %
(tthr, dset_out, dset_out_msk, critical_size, ttest_fn, log_out))
cmd = "".join(cmds)
utils.run_cmds(cmd)
def afni_niml_zscore_makefull_wizard(cfg):
# ensure we have access to the AFNI binary
instacorrbin = '3dSetupGroupInCorr'
if utils.which(instacorrbin) is None:
raise ValueError("could not locate binary %r" % instacorrbin)
# get configuration values
fns = cfg['filenames']
prefix = cfg['prefix']
group_prefix = cfg['group_prefix']
group_postfix = cfg.get('grouppostfix', None)
if group_postfix is None:
group_postfix = _smart_filename_decode(fns, 'postfix')
if not group_postfix is None:
print "Using automatic postfix %s" % group_postfix
overwrite = cfg['overwrite']
# figure out to where to pad to node to
pad_to_node = cfg.get('pad_to_node', None)
if pad_to_node is None:
pad_to_ico_ld = cfg.get('pad_to_ico_ld', None)
if pad_to_ico_ld is None:
pad_to_ico_ld = _smart_filename_decode(fns, 'pad_to_ico_ld')
if not pad_to_ico_ld is None:
pad_to_node = pad_to_ico_ld * pad_to_ico_ld * 10 + 2
print "Using automatic pad_to_ico_ld=%r, pad_to_node=%r" % (pad_to_ico_ld, pad_to_node)
if pad_to_node:
pad_to_node = int(pad_to_node)
# process each of the input files
fnouts = []
for fn in fns:
[pth, nm] = os.path.split(fn)
fnout = os.path.join(pth, prefix + nm)
if os.path.exists(fnout) and not overwrite:
print("Output file %s already exists, skipping (use '--overwrite' to override)" % fnout)
else:
afni_niml_zscore_makefull(fn, fnout, pad_to_node=pad_to_node)
print "Converted %s -> %s (in %s)" % (nm, prefix + nm, pth)
fnouts.append(fnout)
[pth, nm] = os.path.split(group_prefix)
ext = '.niml.dset'
if ext.endswith(ext):
ext = ext[:(len(nm) - len(ext))]
fullprefix = nm if group_postfix is None else '%s%s' % (nm, group_postfix)
fullname = os.path.join(pth, fullprefix)
cmds = ['cd "%s"; ' % pth]
groupfnsout = ['%s.grpincorr.%s' % (fullname, ext) for ext in ['niml', 'data']]
if any(map(os.path.exists, groupfnsout)):
if overwrite:
cmds.extend('rm %s;' % fn for fn in groupfnsout)
else:
print("Some or all of output files (%s) already exists (use '--overwrite' to override)" % (" ".join(groupfnsout)))
cmds.append('%s -prefix ./%s' % (instacorrbin, fullprefix))
cmds.extend(' %s' % fn for fn in fnouts)
cmd = "".join(cmds)
utils.run_cmds(cmd)
msg = ("\n\nTo view the results in SUMA:\n"
"- open a terminal window\n"
"- run 'cd %s; 3dGroupInCorr -setA %s.grpincorr.niml -suma'\n"
"- open a second terminal window\n"
"- cd to a directory with surfaces, run 'suma -spec SPECFILE.spec -niml '\n"
"- in SUMA, select a node while holding down ctrl+shift" %
(pth, fullprefix))
print msg
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses align_epi_anat.py
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
fullext = config['outvol_fullext']
ext = config['outvol_ext']
if config['sid'] is None:
raise ValueError('Need sid')
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol%(outvol_fullext)s' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol%(sssuffix)s%(outvol_fullext)s' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s%s' % (refdir, e_n, fullext)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s%s' % (ssalprefix, fullext),
fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all(
[os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
alignedfn = '%s/%s%s' % (refdir, ssalprefix, fullext)
if config['identity']:
fullmatrix_content = '"MATRIX(%s)"' % unity.replace(" ", ",")
cmd = 'cd "%s"; cat_matvec %s > %s; 3dcopy -overwrite %s%s %s%s%s' % (
refdir, fullmatrix_content, fullmatrixfn, a_n, ext, a_n,
alignsuffix, ext)
else:
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = (
'-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None'
if config['isepi'] else
'-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None'
)
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
if config['template']:
aea_opts += " -Allineate_opts '-maxrot 10 -maxshf 10 -maxscl 1.5'"
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (
refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
cmds.append(_set_vol_space_cmd(alignedfn, config))
utils.run_cmds(cmds, env)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' %
(refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' %
(refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s%s' % (refdir, alprefix, fullext)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append(
'cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s'
% (refdir, newgrid, matrixfn, alprefix, surfvolfn))
cmds.append(
_set_vol_space_cmd('%s/%s+orig' % (refdir, alprefix), config))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s%s' % (f, fullext) for f in [ssalprefix, alprefix]]
headernukefields = [
'ALLINEATE_MATVEC_B2S_000000', 'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000', 'WARPDRIVE_MATVEC_INV_000000'
]
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (
refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
utils.run_cmds('; '.join(cmds), env)
cmds = []
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
use_ss = config['expvol_ss']
# ae_{e,s}_n are AddEdge names for expvol and surfvol
ae_e_n = utils.afni_fileparts(config['expvol'])[1]
if use_ss:
ae_e_n += config['sssuffix']
ae_s_n = ssalprefix #if use_ss else alprefix
# *_ne have the output extension as well
ae_e_ne = ae_e_n + ext
ae_s_ne = ae_s_n + ext
addedge_fns = ['%s/_ae.ExamineList.log' % refdir]
exts = ['HEAD', 'BRIK']
orig_ext = '+orig'
addedge_rootfns = [
'%s_%s%%s' % (ae_e_n, postfix)
for postfix in ['e3', 'ec', ae_s_n + '_ec']
]
addedge_rootfns.extend(
['%s_%s%%s' % (ae_s_n, postfix) for postfix in ['e3', 'ec']])
addedge_fns_pat = [
'%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts
]
addegde_pathfns_orig = map(lambda x: os.path.join(refdir, x % '+orig'),
addedge_fns_pat) + addedge_fns
addegde_pathfns_ext = map(lambda x: os.path.join(refdir, x % ext),
addedge_fns_pat)
addegde_exists = map(os.path.exists, addegde_pathfns_ext)
if overwrite or not all(addegde_exists):
ae_ns = (ae_e_n, ae_s_n)
cmds.extend(
map(lambda fn: 'if [ -e "%s" ]; then rm "%s"; fi' % (fn, fn),
addegde_pathfns_orig + addegde_pathfns_ext))
cmds.append(';'.join(['cd %s' % refdir] + [
_convert_vol_space_to_orig_cmd('%s/%s%s' % (refdir, n, ext))
for n in ae_ns
] + ['\@AddEdge %s+orig %s+orig' % ae_ns]))
set_space_fns = addegde_pathfns_orig + [
'%s/%s%s.%s' % (refdir, fn, orig_ext, exts[0]) for fn in ae_ns
]
for fn in set_space_fns: #['%s/%s' % (refdir, fn % orig_ext) for fn in addedge_fns_pat]:
if fn.endswith('.log'):
continue
cmds.append('if [ -e %s ]; then %s; fi' %
(fn, _set_vol_space_cmd(fn, config)))
utils.run_cmds(cmds, env)
cmds = []
else:
print "AddEdge seems to have been run already"
sid = config['sid']
plot_slice_fns = [
(ae_e_n + '_e3', ae_s_n + '_e3', '%s_qa_e3.png' % sid),
(None, ae_e_n + '_' + ae_s_n + '_ec', '%s_qa_ec.png' % sid)
]
plot_slice_imgfns = ['%s/%s' % (refdir, fn) for fn in plot_slice_fns]
if overwrite or not all(map(os.path.exists, plot_slice_imgfns)):
slice_dims = [0, 1, 2]
slice_pos = [.35, .45, .55, .65]
for fns in plot_slice_fns:
input_fns = []
for i, fn in enumerate(fns):
if fn is not None:
fn = '%s/%s' % (refdir, fn)
if i <= 1:
fn += ext
input_fns.append(fn)
fn1, fn2, fnout = input_fns
if not os.path.exists(fnout):
_make_slice_plot(fn1, fn2, fnout)
print "QA Image saved to %s" % fnout
else:
print "Already exists: %s" % fnout
else:
print "QA images already exist"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = (
'cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
origext = '.asc'
ext = format2extension(config)
tp = format2type(config)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*%s' % (config['mi_icopat'] % icold, hemi, origext)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
if not sumafile.endswith(origext):
raise ValueError("%s does not end with %s" %
(sumafile, origext))
#s = sumafile.split(".")
#s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
#alsumafile = ".".join(s)
extsumafile = sumafile[:-len(origext)]
alsumafile = extsumafile + config['alsuffix'] + ext
if config['overwrite'] or not os.path.exists(
'%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_%s ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, tp, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg%s' % (pat, ext)):
sumaout = '%s/%s' % (refdir, extsumafile + ext)
if config['overwrite'] or not os.path.exists(sumaout):
s = surf.read('%s/%s' % (sumadir, sumafile))
surf.write(s, sumaout)
#cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = os.path.join(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = os.path.join(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def run_makesurfmasks(config, env):
refdir = config["refdir"]
overwrite = config["overwrite"]
if config["sid"] is None:
raise ValueError("Need sid")
sumfn = "%s_qa_surf_mask" % config["sid"] # output file
fullext = config["outvol_fullext"]
volor = config["outvol_ext"]
sumfn_path = "%s/%s%s" % (refdir, sumfn, fullext)
qafn_path = "%s/%s.png" % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ["%s%s" % (volor, e) for e in ".HEAD", ".BRIK*"]
sssuffix = config["sssuffix"] if config["expvol_ss"] else ""
expvol_fn = "%s%s%s" % (utils.afni_fileparts(config["expvol"])[1], sssuffix, volor)
# if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ["l", "r"]:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = "__t.1D"
oneDtfn = "__tt.1D" # transposed
cmds = [
"cd %s" % refdir,
"1deval -1D: -num %d -expr 1 > %s" % (icold ** 2 * 10 + 1, oneDfn),
"1dtranspose %s > %s" % (oneDfn, oneDtfn),
]
utils.run_cmds(";".join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = (
'3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
" -grid_parent %s. -prefix %%s -sdata %s -overwrite"
) % (expvol_fn, expvol_fn, oneDtfn)
infix2val = {"-surf_A pial": 1, "-surf_A smoothwm": 2, "-surf_A smoothwm -surf_B pial -f_steps 20": 4}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi, config["alsuffix"])
for infix, val in infix2val.iteritems():
fnprefix = "__m%d_%sh" % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds("cd %s;%s" % (refdir, cmd))
tmpfns.extend(["%s%s" % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ["cd %s" % refdir]
catfn = "__cat"
cmds.extend(
[
"3dTcat -overwrite -prefix %s %s" % (catfn, " ".join(volfns)),
"3dTstat -overwrite -sum -prefix %s %s%s" % (sumfn, catfn, volor),
]
)
tmpfns.extend(["%s%s" % (catfn, e) for e in volexts])
cmds.extend("rm %s" % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(";".join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = "%s/%s" % (refdir, expvol_fn)
_make_slice_plot(expvol_path, sumfn_path, qafn_path)
def afni_niml_zscore_makefull_wizard(cfg):
# ensure we have access to the AFNI binary
instacorrbin = '3dSetupGroupInCorr'
if utils.which(instacorrbin) is None:
raise ValueError("could not locate binary %r" % instacorrbin)
# get configuration values
fns = cfg['filenames']
prefix = cfg['prefix']
group_prefix = cfg['group_prefix']
group_postfix = cfg.get('grouppostfix', None)
if group_postfix is None:
group_postfix = _smart_filename_decode(fns, 'postfix')
if not group_postfix is None:
print "Using automatic postfix %s" % group_postfix
overwrite = cfg['overwrite']
# figure out to where to pad to node to
pad_to_node = cfg.get('pad_to_node', None)
if pad_to_node is None:
pad_to_ico_ld = cfg.get('pad_to_ico_ld', None)
if pad_to_ico_ld is None:
pad_to_ico_ld = _smart_filename_decode(fns, 'pad_to_ico_ld')
if not pad_to_ico_ld is None:
pad_to_node = pad_to_ico_ld * pad_to_ico_ld * 10 + 2
print "Using automatic pad_to_ico_ld=%r, pad_to_node=%r" % (pad_to_ico_ld, pad_to_node)
if pad_to_node:
pad_to_node = int(pad_to_node)
# process each of the input files
fnouts = []
for fn in fns:
[pth, nm] = os.path.split(fn)
fnout = pathjoin(pth, prefix + nm)
if os.path.exists(fnout) and not overwrite:
print("Output file %s already exists, skipping (use '--overwrite' to override)" % fnout)
else:
afni_niml_zscore_makefull(fn, fnout, pad_to_node=pad_to_node)
print "Converted %s -> %s (in %s)" % (nm, prefix + nm, pth)
fnouts.append(fnout)
[pth, nm] = os.path.split(group_prefix)
ext = '.niml.dset'
if ext.endswith(ext):
ext = ext[:(len(nm) - len(ext))]
fullprefix = nm if group_postfix is None else '%s%s' % (nm, group_postfix)
fullname = pathjoin(pth, fullprefix)
cmds = ['cd "%s"; ' % pth]
groupfnsout = ['%s.grpincorr.%s' % (fullname, ext) for ext in ['niml', 'data']]
if any(map(os.path.exists, groupfnsout)):
if overwrite:
cmds.extend('rm %s;' % fn for fn in groupfnsout)
else:
print("Some or all of output files (%s) already exists (use '--overwrite' to override)" % (" ".join(groupfnsout)))
cmds.append('%s -prefix ./%s' % (instacorrbin, fullprefix))
cmds.extend(' %s' % fn for fn in fnouts)
cmd = "".join(cmds)
utils.run_cmds(cmd)
msg = ("\n\nTo view the results in SUMA:\n"
"- open a terminal window\n"
"- run 'cd %s; 3dGroupInCorr -setA %s.grpincorr.niml -suma'\n"
"- open a second terminal window\n"
"- cd to a directory with surfaces, run 'suma -spec SPECFILE.spec -niml '\n"
"- in SUMA, select a node while holding down ctrl+shift" %
(pth, fullprefix))
print msg
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses @SUMA_AlignToExperiment
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol+orig.HEAD' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol_ss+orig.HEAD' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s+orig.HEAD' % (refdir, e_n)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
if config['identity']:
fullmatrixfn = '"MATRIX(%s)"' % unity.replace(" ", ",")
else:
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s+orig.HEAD' % ssalprefix,
fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all(
[os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = (
'-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None'
if config['isepi'] else
'-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None'
)
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (
refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
utils.run_cmds(cmds, env)
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' %
(refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' %
(refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s+orig.HEAD' % (refdir, alprefix)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append(
'cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s'
% (refdir, newgrid, matrixfn, alprefix, surfvolfn))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s+orig.HEAD' % f for f in [ssalprefix, alprefix]]
headernukefields = [
'ALLINEATE_MATVEC_B2S_000000', 'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000', 'WARPDRIVE_MATVEC_INV_000000'
]
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (
refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
basedset = volsin[1]
[d, n, o, e] = utils.afni_fileparts(basedset)
if 'nii' in e:
o = '+orig'
if overwrite or not os.path.exists('%s/%s+orig.HEAD' % refdir, n):
cmds.append('cd %s; 3dcopy -overwrite %s.nii %s%s' %
(refdir, n, n, o))
dset = '%s+orig.HEAD' % alprefix
n_dset = utils.afni_fileparts(dset)[1]
addedge_fns = ['_ae.ExamineList.log']
exts = ['HEAD', 'BRIK']
addedge_rootfns = [
'%s_%s+orig' % (n, postfix)
for postfix in ['e3', 'ec', n_dset + '_ec']
]
addedge_rootfns.extend(
['%s_%s+orig' % (n_dset, postfix) for postfix in ['e3', 'ec']])
addedge_fns = [
'%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts
]
addegde_pathfns = map(lambda x: os.path.join(refdir, x), addedge_fns)
addegde_exists = map(os.path.exists, addegde_pathfns)
if overwrite or not all(addegde_exists):
if overwrite:
cmds.extend(map(lambda fn: 'rm "%s"' % fn, addegde_pathfns))
cmds.append('cd %s; \@AddEdge %s%s %s' % (refdir, n, o, dset))
else:
print "AddEdge seems to have been run already"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = (
'cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*.asc' % (config['mi_icopat'] % icold, hemi)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
s = sumafile.split(".")
s[len(s) - 2] += config[
'alsuffix'] # insert '_al' just before last dot
alsumafile = ".".join(s)
if config['overwrite'] or not os.path.exists(
'%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_fs ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg.asc' % pat):
if config['overwrite'] or not os.path.exists(
'%s/%s' % (refdir, sumafile)):
cmds.append('cp %s/%s %s/%s' %
(sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = os.path.join(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = os.path.join(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
if config['identity']:
return
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn) for fn in ['brain.nii', 'T1.nii']]
surfvol_trgs = [
'%s/%s' % (refdir, fn) for fn in
['%s_SurfVol_ss+orig.HEAD' %
sid, '%s_SurfVol+orig.HEAD' % sid]
]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dcopy -overwrite %s ./%s' %
(refdir, src, trg_short))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
if 'nii' in e_e:
# ensure e_n+orig is in refdir
if overwrite or not utils.afni_fileexists('%s/%s+orig.HEAD' %
(refdir, e_n)):
print "Converting %s from NIFTI to AFNI format" % e_n
cmds.append('cd "%s"; 3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, e_n, expvol_src))
cmds.append(
'if [ -e %s/%s+tlrc.HEAD ]; then 3drefit -view orig -space ORIG %s/%s+tlrc; else echo "File in orig orientation - no refit necessary"; fi'
% (refdir, e_n, refdir, e_n))
expvol_src = '%s/%s+orig.HEAD' % (refdir, e_n)
expvol_trg = '%s/%s+orig.HEAD' % (refdir, expvol_trg_prefix)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append(
'cd "%s";3dSkullStrip -overwrite -prefix ./%s+orig -input %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s+orig %s' %
(refdir, expvol_trg_prefix, expvol_src))
else:
print "No skull strip because already exists: %s+orig" % expvol_trg_prefix
utils.run_cmds(cmds, env)
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses @SUMA_AlignToExperiment
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol+orig.HEAD' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol_ss+orig.HEAD' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s+orig.HEAD' % (refdir, e_n)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
if config['identity']:
fullmatrixfn = '"MATRIX(%s)"' % unity.replace(" ", ",")
else:
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s+orig.HEAD' % ssalprefix, fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all([os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = ('-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None' if config['isepi']
else '-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None')
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
utils.run_cmds(cmds, env)
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' % (refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' % (refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s+orig.HEAD' % (refdir, alprefix)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append('cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s' %
(refdir, newgrid, matrixfn, alprefix, surfvolfn))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s+orig.HEAD' % f for f in [ssalprefix, alprefix]]
headernukefields = ['ALLINEATE_MATVEC_B2S_000000',
'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000',
'WARPDRIVE_MATVEC_INV_000000']
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
basedset = volsin[1]
[d, n, o, e] = utils.afni_fileparts(basedset)
if 'nii' in e:
o = '+orig'
if overwrite or not os.path.exists('%s/%s+orig.HEAD' % refdir, n):
cmds.append('cd %s; 3dcopy -overwrite %s.nii %s%s' % (refdir, n, n, o))
dset = '%s+orig.HEAD' % alprefix
n_dset = utils.afni_fileparts(dset)[1]
addedge_fns = ['_ae.ExamineList.log']
exts = ['HEAD', 'BRIK']
addedge_rootfns = ['%s_%s+orig' % (n, postfix)
for postfix in ['e3', 'ec', n_dset + '_ec']]
addedge_rootfns.extend(['%s_%s+orig' % (n_dset, postfix)
for postfix in ['e3', 'ec']])
addedge_fns = ['%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts]
addegde_pathfns = map(lambda x:os.path.join(refdir, x), addedge_fns)
addegde_exists = map(os.path.exists, addegde_pathfns)
if overwrite or not all(addegde_exists):
if overwrite:
cmds.extend(map(lambda fn : 'rm "%s"' % fn, addegde_pathfns))
cmds.append('cd %s; \@AddEdge %s%s %s' % (refdir, n, o, dset))
else:
print "AddEdge seems to have been run already"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = ('cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*.asc' % (config['mi_icopat'] % icold, hemi)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
s = sumafile.split(".")
s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
alsumafile = ".".join(s)
if config['overwrite'] or not os.path.exists('%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_fs ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg.asc' % pat):
if config['overwrite'] or not os.path.exists('%s/%s' % (refdir, sumafile)):
cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = os.path.join(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = os.path.join(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
fullext = config['outvol_fullext']
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn) for fn in ['brain.nii', 'T1.nii']]
surfvol_trgs = [
'%s/%s' % (refdir, fn) for fn in
['%s_SurfVol_ss%s' % (sid, fullext),
'%s_SurfVol%s' % (sid, fullext)]
]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append(
'cd "%s"; 3dresample -overwrite -orient LPI -inset %s -prefix ./%s'
% (refdir, src, trg_short))
cmds.append(
_set_vol_space_cmd('%s/%s+orig' % (refdir, t_n), config))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
expvol_trg_tmp_prefix = '__tmp_%s' % expvol_trg_prefix
expvol_trg = '%s/%s%s' % (refdir, expvol_trg_prefix, fullext)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
ext = config['outvol_ext']
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append(
'cd "%s";3dSkullStrip -overwrite -prefix ./%s%s -input %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s%s %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
cmds.append(
'cd "%s"; 3dresample -overwrite -orient LPI -prefix %s -inset %s%s'
% (refdir, expvol_trg_prefix, expvol_trg_tmp_prefix, ext))
cmds.append('rm %s/%s*' % (refdir, expvol_trg_tmp_prefix))
cmds.append(_set_vol_space_cmd(expvol_trg, config))
else:
print "No skull strip because already exists: %s%s" % (
expvol_trg_prefix, ext)
utils.run_cmds(cmds, env)
def run_skullstrip(config, env):
fullext = config['outvol_fullext']
overwrite = config['overwrite']
refdir = config['refdir']
cmds = []
if not os.path.exists(refdir):
cmds.append('mkdir %(refdir)s' % config)
sumadir = config['sumadir']
sid = config['sid']
fs_sid = config['fs_sid']
if not sid:
raise ValueError("Subject id is not set, cannot continue")
# process the surfvol anatomical.
# because it's already skull stripped by freesurfer
# simply copy it over; rename brain.nii to surfvol_ss
surfvol_srcs = ['%s/%s' % (sumadir, fn)
for fn in ['brain.nii',
'T1.nii']]
surfvol_trgs = ['%s/%s' % (refdir, fn)
for fn in ['%s_SurfVol_ss%s' % (sid, fullext),
'%s_SurfVol%s' % (sid, fullext)]]
for src, trg in zip(surfvol_srcs, surfvol_trgs):
if os.path.exists(trg) and not overwrite:
print '%s already exists' % trg
else:
t_p, t_n, t_o, t_e = utils.afni_fileparts(trg)
trg_short = '%s%s' % (t_n, t_o)
cmds.append('cd "%s"; 3dresample -overwrite -orient LPI -inset %s -prefix ./%s' %
(refdir, src, trg_short))
cmds.append(_set_vol_space_cmd('%s/%s+orig' % (refdir, t_n), config))
# process experimental volume.
expvol_src = config['expvol']
do_ss = config['expvol_ss']
[e_p, e_n, e_o, e_e] = utils.afni_fileparts(expvol_src)
expvol_trg_prefix = '%s%s' % (e_n, config['sssuffix'] if do_ss else '')
expvol_trg_tmp_prefix = '__tmp_%s' % expvol_trg_prefix
expvol_trg = '%s/%s%s' % (refdir, expvol_trg_prefix, fullext)
print "Attempt %s -> %s" % (expvol_src, expvol_trg)
ext = config['outvol_ext']
if overwrite or not utils.afni_fileexists(expvol_trg):
if do_ss:
cmds.append('cd "%s";3dSkullStrip -overwrite -prefix ./%s%s -input %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
else:
cmds.append('cd "%s";3dbucket -overwrite -prefix ./%s%s %s' %
(refdir, expvol_trg_tmp_prefix, ext, expvol_src))
cmds.append('cd "%s"; 3dresample -overwrite -orient LPI -prefix %s -inset %s%s' %
(refdir, expvol_trg_prefix, expvol_trg_tmp_prefix, ext))
cmds.append('rm %s/%s*' % (refdir, expvol_trg_tmp_prefix))
cmds.append(_set_vol_space_cmd(expvol_trg, config))
else:
print "No skull strip because already exists: %s%s" % (expvol_trg_prefix, ext)
utils.run_cmds(cmds, env)
def run_makesurfmasks(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
if config['sid'] is None:
raise ValueError('Need sid')
sumfn = '%s_qa_surf_mask' % config['sid'] # output file
fullext = config['outvol_fullext']
volor = config['outvol_ext']
sumfn_path = '%s/%s%s' % (refdir, sumfn, fullext)
qafn_path = '%s/%s.png' % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ['%s%s' % (volor, e) for e in '.HEAD', '.BRIK*']
sssuffix = config['sssuffix'] if config['expvol_ss'] else ''
expvol_fn = '%s%s%s' % (utils.afni_fileparts(
config['expvol'])[1], sssuffix, volor)
#if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = '__t.1D'
oneDtfn = '__tt.1D' # transposed
cmds = [
'cd %s' % refdir,
'1deval -1D: -num %d -expr 1 > %s' % (icold**2 * 10 + 1, oneDfn),
'1dtranspose %s > %s' % (oneDfn, oneDtfn)
]
utils.run_cmds(';'.join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = ('3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
' -grid_parent %s. -prefix %%s -sdata %s -overwrite') % \
(expvol_fn, expvol_fn, oneDtfn)
infix2val = {
'-surf_A pial': 1,
'-surf_A smoothwm': 2,
'-surf_A smoothwm -surf_B pial -f_steps 20': 4
}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
for infix, val in infix2val.iteritems():
fnprefix = '__m%d_%sh' % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds('cd %s;%s' % (refdir, cmd))
tmpfns.extend(['%s%s' % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ['cd %s' % refdir]
catfn = '__cat'
cmds.extend([
'3dTcat -overwrite -prefix %s %s' % (catfn, ' '.join(volfns)),
'3dTstat -overwrite -sum -prefix %s %s%s' % (sumfn, catfn, volor)
])
tmpfns.extend(['%s%s' % (catfn, e) for e in volexts])
cmds.extend('rm %s' % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(';'.join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = '%s/%s' % (refdir, expvol_fn)
_make_slice_plot(expvol_path, sumfn_path, qafn_path)
def run_alignment(config, env):
'''Aligns anat (which is assumed to be aligned with EPI data) to FreeSurfer SurfVol
This function strips the anatomicals (by default), then uses align_epi_anat.py
to estimate the alignment, then applies this transformation to the non-skull-stripped
SurfVol and also to the surfaces. Some alignment headers will be nuked'''
overwrite = config['overwrite']
alignsuffix = config['al2expsuffix']
refdir = config['refdir']
fullext = config['outvol_fullext']
ext = config['outvol_ext']
if config['sid'] is None:
raise ValueError('Need sid')
cmds = []
if not os.path.exists(config['refdir']):
cmds.append('mkdir %(refdir)s' % config)
# two volumes may have to be stripped: the inpput anatomical, and the surfvol.
# put them in a list here and process them similarly
surfvol = '%(refdir)s/%(sid)s_SurfVol%(outvol_fullext)s' % config
surfvol_ss = '%(refdir)s/%(sid)s_SurfVol%(sssuffix)s%(outvol_fullext)s' % config
e_p, e_n, _, _ = utils.afni_fileparts(config['expvol'])
if config['expvol_ss']:
e_n = '%s%s' % (e_n, config['sssuffix'])
expvol = '%s/%s%s' % (refdir, e_n, fullext)
volsin = [surfvol_ss, expvol]
for volin in volsin:
if not os.path.exists(volin):
raise ValueError('File %s does not exist' % volin)
a_n = utils.afni_fileparts(volsin[0])[1] # surfvol input root name
ssalprefix = '%s%s' % (a_n, alignsuffix)
unity = "1 0 0 0 0 1 0 0 0 0 1 0" # we all like unity, don't we?
fullmatrixfn = '%s_mat.aff12.1D' % ssalprefix
aloutfns = ['%s%s' % (ssalprefix, fullext), fullmatrixfn] # expected output files if alignment worked
if config['overwrite'] or not all([os.path.exists('%s/%s' % (refdir, f)) for f in aloutfns]):
alignedfn = '%s/%s%s' % (refdir, ssalprefix, fullext)
if config['identity']:
fullmatrix_content = '"MATRIX(%s)"' % unity.replace(" ", ",")
cmd = 'cd "%s"; cat_matvec %s > %s; 3dcopy -overwrite %s%s %s%s%s' % (refdir, fullmatrix_content, fullmatrixfn, a_n, ext, a_n, alignsuffix, ext)
else:
# use different inputs depending on whether expvol is EPI or ANAT
twovolpat = ('-anat %s -epi %s -anat2epi -epi_base 0 -anat_has_skull no -epi_strip None' if config['isepi']
else '-dset1 %s -dset2 %s -dset1to2 -dset1_strip None -dset2_strip None')
# use this pattern to generate a suffix
twovolsuffix = twovolpat % (volsin[0], volsin[1])
aea_opts = config['aea_opts']
if config['template']:
aea_opts += " -Allineate_opts '-maxrot 10 -maxshf 10 -maxscl 1.5'"
# align_epi_anat.py
cmd = 'cd "%s"; align_epi_anat.py -overwrite -suffix %s %s %s' % (refdir, alignsuffix, twovolsuffix, aea_opts)
cmds.append(cmd)
cmds.append(_set_vol_space_cmd(alignedfn, config))
utils.run_cmds(cmds, env)
else:
print "Alignment already done - skipping"
# run these commands first, then check if everything worked properly
cmds = []
# see if the expected transformation file was found
if not config['identity'] and not os.path.exists('%s/%s' % (refdir, fullmatrixfn)):
raise Exception("Could not find %s in %s" % (fullmatrixfn, refdir))
# now make a 3x4 matrix
matrixfn = '%s%s.A2E.1D' % (a_n, alignsuffix)
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn)):
cmds.append('cd "%s"; cat_matvec %s > %s || exit 1' % (refdir, fullmatrixfn, matrixfn))
# make an aligned, non-skullstripped version of SurfVol in refdir
alprefix = '%s_SurfVol%s' % (config['sid'], alignsuffix)
svalignedfn = '%s/%s%s' % (refdir, alprefix, fullext)
newgrid = 1 # size of anatomical grid in mm. We'll have to resample, otherwise 3dWarp does
# not respect the corners of the volume (as of April 2012)
if overwrite or not os.path.exists(svalignedfn):
#if not config['fs_sid']:
# raise ValueError("Don't have a freesurfer subject id - cannot continue")
#surfvolfn = '%s/%s_SurfVol+orig' % (config['sumadir'], config['fs_sid'])
surfvolfn = '%s/T1.nii' % config['sumadir']
cmds.append('cd "%s";3dWarp -overwrite -newgrid %f -matvec_out2in `cat_matvec -MATRIX %s` -prefix ./%s %s' %
(refdir, newgrid, matrixfn, alprefix, surfvolfn))
cmds.append(_set_vol_space_cmd('%s/%s+orig' % (refdir, alprefix), config))
else:
print '%s already exists - skipping Warp' % svalignedfn
utils.run_cmds(cmds, env)
cmds = []
# nuke afni headers
headernukefns = ['%s%s' % (f, fullext) for f in [ssalprefix, alprefix]]
headernukefields = ['ALLINEATE_MATVEC_B2S_000000',
'ALLINEATE_MATVEC_S2B_000000',
'WARPDRIVE_MATVEC_FOR_000000',
'WARPDRIVE_MATVEC_INV_000000']
for fn in headernukefns:
for field in headernukefields:
# nuke transformation - otherwise AFNI does this unwanted transformation for us
fullfn = '%s/%s' % (refdir, fn)
if not (os.path.exists(fullfn) or config['identity']):
raise ValueError("File %r does not exist" % fullfn)
refitcmd = "3drefit -atrfloat %s '%s' %s" % (field, unity, fn)
# only refit if not already in AFNI history (which is stored in HEADfile)
cmd = 'cd "%s"; m=`grep "%s" %s | wc -w`; if [ $m -eq 0 ]; then %s; else echo "File %s seems already 3drefitted"; fi' % (refdir, refitcmd, fn, refitcmd, fn)
cmds.append(cmd)
utils.run_cmds('; '.join(cmds), env)
cmds = []
# run AddEdge so that volumes can be inspected visually for alignment
if config['AddEdge']:
use_ss = config['expvol_ss']
# ae_{e,s}_n are AddEdge names for expvol and surfvol
ae_e_n = utils.afni_fileparts(config['expvol'])[1]
if use_ss:
ae_e_n += config['sssuffix']
ae_s_n = ssalprefix #if use_ss else alprefix
# *_ne have the output extension as well
ae_e_ne = ae_e_n + ext
ae_s_ne = ae_s_n + ext
addedge_fns = ['%s/_ae.ExamineList.log' % refdir]
exts = ['HEAD', 'BRIK']
orig_ext = '+orig'
addedge_rootfns = ['%s_%s%%s' % (ae_e_n, postfix)
for postfix in ['e3', 'ec', ae_s_n + '_ec']]
addedge_rootfns.extend(['%s_%s%%s' % (ae_s_n, postfix)
for postfix in ['e3', 'ec']])
addedge_fns_pat = ['%s.%s' % (fn, e) for fn in addedge_rootfns for e in exts]
addegde_pathfns_orig = map(lambda x:pathjoin(refdir, x % '+orig'), addedge_fns_pat) + addedge_fns
addegde_pathfns_ext = map(lambda x:pathjoin(refdir, x % ext), addedge_fns_pat)
addegde_exists = map(os.path.exists, addegde_pathfns_ext)
if overwrite or not all(addegde_exists):
ae_ns = (ae_e_n, ae_s_n)
cmds.extend(map(lambda fn : 'if [ -e "%s" ]; then rm "%s"; fi' % (fn, fn), addegde_pathfns_orig + addegde_pathfns_ext))
cmds.append(';'.join(['cd %s' % refdir] +
[_convert_vol_space_to_orig_cmd('%s/%s%s' % (refdir, n, ext))
for n in ae_ns] +
['\@AddEdge %s+orig %s+orig' % ae_ns]))
set_space_fns = addegde_pathfns_orig + ['%s/%s%s.%s' % (refdir, fn, orig_ext, exts[0]) for fn in ae_ns]
for fn in set_space_fns: #['%s/%s' % (refdir, fn % orig_ext) for fn in addedge_fns_pat]:
if fn.endswith('.log'):
continue
cmds.append('if [ -e %s ]; then %s; fi' % (fn, _set_vol_space_cmd(fn, config)))
utils.run_cmds(cmds, env)
cmds = []
else:
print "AddEdge seems to have been run already"
sid = config['sid']
plot_slice_fns = [(ae_e_n + '_e3', ae_s_n + '_e3', '%s_qa_e3.png' % sid),
(None, ae_e_n + '_' + ae_s_n + '_ec', '%s_qa_ec.png' % sid)]
plot_slice_imgfns = ['%s/%s' % (refdir, fn) for fn in plot_slice_fns]
if overwrite or not all(map(os.path.exists, plot_slice_imgfns)):
slice_dims = [0, 1, 2]
slice_pos = [.35, .45, .55, .65]
for fns in plot_slice_fns:
input_fns = []
for i, fn in enumerate(fns):
if fn is not None:
fn = '%s/%s' % (refdir, fn)
if i <= 1:
fn += ext
input_fns.append(fn)
fn1, fn2, fnout = input_fns
if not os.path.exists(fnout):
_make_slice_plot(fn1, fn2, fnout)
print "QA Image saved to %s" % fnout
else:
print "Already exists: %s" % fnout
else:
print "QA images already exist"
# because AFNI uses RAI orientation but FreeSurfer LPI, make a new
# affine transformation matrix in which the signs of
# x and y coordinates are negated before and after the transformation
matrixfn_LPI2RAI = '%s.A2E_LPI.1D' % ssalprefix
if overwrite or not os.path.exists('%s/%s' % (refdir, matrixfn_LPI2RAI)):
lpirai = '"MATRIX(-1,0,0,0,0,-1,0,0,0,0,1,0)"'
cmd = ('cd %s; cat_matvec -ONELINE %s `cat_matvec -MATRIX %s` %s > %s' %
(refdir, lpirai, matrixfn, lpirai, matrixfn_LPI2RAI))
cmds.append(cmd)
# apply transformation to surfaces
[icolds, hemis] = _get_hemis_icolds(config)
sumadir = config['sumadir']
sumafiles = os.listdir(sumadir)
origext = '.asc'
ext = format2extension(config)
tp = format2type(config)
# process all hemispheres and ld values
for icold in icolds:
for hemi in hemis:
pat = '%s%sh.?*%s' % (config['mi_icopat'] % icold, hemi, origext)
for sumafile in sumafiles:
if fnmatch.fnmatch(sumafile, pat):
if not sumafile.endswith(origext):
raise ValueError("%s does not end with %s" % (sumafile, origext))
#s = sumafile.split(".")
#s[len(s) - 2] += config['alsuffix'] # insert '_al' just before last dot
#alsumafile = ".".join(s)
extsumafile = sumafile[:-len(origext)]
alsumafile = extsumafile + config['alsuffix'] + ext
if config['overwrite'] or not os.path.exists('%s/%s' % (refdir, alsumafile)):
# now apply transformation
cmd = 'cd "%s";ConvertSurface -overwrite -i_fs %s/%s -o_%s ./%s -ixmat_1D %s' % \
(refdir, sumadir, sumafile, tp, alsumafile, matrixfn_LPI2RAI)
cmds.append(cmd)
# as of June 2012 copy the original sphere.reg (not aligned) as well
if sumafile == ('%s.sphere.reg%s' % (pat, ext)):
sumaout = '%s/%s' % (refdir, extsumafile + ext)
if config['overwrite'] or not os.path.exists(sumaout):
s = surf.read('%s/%s' % (sumadir, sumafile))
surf.write(s, sumaout)
#cmds.append('cp %s/%s %s/%s' % (sumadir, sumafile, refdir, sumafile))
mapfn = (config['mi_icopat'] % icold) + config['hemimappingsuffix']
srcpathfn = pathjoin(sumadir, mapfn)
if os.path.exists(srcpathfn):
trgpathfn = pathjoin(refdir, mapfn)
if not os.path.exists(trgpathfn) or config['overwrite']:
cmds.append('cp %s %s' % (srcpathfn, trgpathfn))
utils.run_cmds(cmds, env)
def null_clustersize(config):
# helper function - called by critical_clustersize
# computes maxmimum cluster size of a single null permutation
output_dir = config['output_dir']
tthr = config['tthr']
fwhm = config['fwhm']
buck_fn_1D = config['buck_fn_1D']
msk = _mask_expr(config)
is_surf = _is_surf(config)
if is_surf:
surf_fn = config['surface_file']
ext, ext1D = _ext(config), _ext(config, for1D=True)
ns = len(config['data_files'])
cmds = ['cd "%s"' % output_dir]
# generate N random data files (N=number of participants)
# use the output bucket to get datasets with the right size
null_fns = []
for i in range(ns):
fn = _fn(config, 'rand_%d' % i, ext1D)
if is_surf:
cmds.append("; 1deval -ok_1D_text -a %s'[0]' -expr 'gran(0,1)' > '%s'" % (buck_fn_1D, fn))
else:
cmds.append("; 3dcalc -overwrite -prefix %s -a %s'[0]' -expr 'gran(0,1)'" % (fn, buck_fn_1D))
null_fns.append(fn)
# bucket random data
buck_fn = _fn(config, 'rand_buck', ext1D)
null_fns_list = ' '.join(null_fns)
if is_surf:
cmds.append('; 1dcat %s > "%s"' % (null_fns_list, buck_fn))
else:
cmds.append('; 3dbucket -overwrite -prefix %s %s' % (buck_fn, null_fns_list))
# smooth all data at once, using estimated FWHM
smooth_fn = _fn(config, 'rand_buck_smooth', ext1D)
if is_surf:
if config['sigma'] > 0:
sigma_str = '-sigma %s' % config['sigma']
else:
sigma_str = ''
cmds.append('; SurfSmooth -overwrite %s -met HEAT_07 -i_fs %s -input %s '
' -fwhm %f -output %s %s' % (msk, surf_fn, buck_fn, fwhm, smooth_fn, sigma_str))
else:
cmds.append('; 3dBlurInMask -overwrite %s -FWHM %f -prefix %s -input %s' %
(msk, fwhm, smooth_fn, buck_fn))
# run ttest
if is_surf:
msk = '' # cannot use mask on surface, but that's fine
# as it was used in SurfSmooth
ttest_fn = _fn(config, 'rand_buck_smooth_t', ext1D)
cmds.append('; 3dttest++ %s -overwrite -prefix %s -setA %s' %
(msk, ttest_fn, smooth_fn))
# extract maximum cluster size (in mm^2 or number of voxels) from output
# and pipe into size_fn
size_fn = _fn(config, 'rand_size', '.1D')
if is_surf:
postfix = "| grep --invert-match '#' | head -1 | cut -c 18-28"
cmds.append('; SurfClust -i_fs %s -input %s 1 -rmm -1 '
' -thresh %f -thresh_col 1 %s > "%s"' %
(surf_fn, ttest_fn, tthr, postfix, size_fn))
else:
postfix = " | grep --invert-match '#' | head -1 | cut -c1-8"
cmds.append("; 3dclust -quiet -1noneg -1clip %f 0 0 %s'[1]' %s > '%s'" %
(tthr, ttest_fn, postfix, size_fn))
utils.run_cmds(''.join(cmds))
# read maximum cluster size form size_fn
sz_str = None
with open(pathjoin(output_dir, size_fn)) as f:
sz_str = f.read()
try:
sz = float(sz_str)
except:
sz = 0. # CHECKME whether this makes sense
print("Null data: maximum size %f" % sz)
if is_surf:
smoothing_fn_rec = pathjoin(output_dir, _fn(config, 'rand_buck_smooth', '.1D.dset.1D.smrec'))
if not os.path.exists(smoothing_fn_rec):
raise ValueError("Smoothing did not succeed. Please check the error"
" messaged. You may have to set sigma manually")
with open(smoothing_fn_rec) as f:
s = f.read()
final_fwhm = float(s.split()[-2])
ratio = fwhm / final_fwhm
thr = 0.9
if ratio < thr or 1. / ratio < thr:
raise ValueError('FWHM converged to %s but expected %s. Consider '
'setting sigma manually' % (final_fwhm, fwhm))
# clean up - remove all temporary files
tmpfns = null_fns + [buck_fn, smooth_fn, ttest_fn, size_fn]
_remove_files(config, tmpfns)
return sz
def run_makesurfmasks(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
if config['sid'] is None:
raise ValueError('Need sid')
sumfn = '%s_qa_surf_mask' % config['sid'] # output file
fullext = config['outvol_fullext']
volor = config['outvol_ext']
sumfn_path = '%s/%s%s' % (refdir, sumfn, fullext)
qafn_path = '%s/%s.png' % (refdir, sumfn)
checkfn_paths = (sumfn_path, qafn_path)
if all(map(os.path.exists, checkfn_paths)) and not overwrite:
print "Already exist: %s" % (", ".join(checkfn_paths))
return
icolds, hemis = _get_hemis_icolds(config)
volexts = ['%s%s' % (volor, e) for e in '.HEAD', '.BRIK*']
sssuffix = config['sssuffix'] if config['expvol_ss'] else ''
expvol_fn = '%s%s%s' % (utils.afni_fileparts(config['expvol'])[1],
sssuffix,
volor)
#if overwrite or not os.path.exists('%s/%s' % (refdir, sv_al_nii_fn)):
# cmd = 'cd %s; 3dcopy -overwrite %s %s' % (refdir, sv_al_orig_fn, sv_al_nii_fn)
# utils.run_cmds(cmd, env)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
icold = max(icolds)
oneDfn = '__t.1D'
oneDtfn = '__tt.1D' # transposed
cmds = ['cd %s' % refdir,
'1deval -1D: -num %d -expr 1 > %s' % (icold ** 2 * 10 + 1, oneDfn),
'1dtranspose %s > %s' % (oneDfn, oneDtfn)]
utils.run_cmds(';'.join(cmds), env)
tmpfns = [oneDfn, oneDtfn]
s2v_cmd = ('3dSurf2Vol -map_func mask2 -data_expr "a*%%d" -spec %%s %%s -sv %s'
' -grid_parent %s. -prefix %%s -sdata %s -overwrite') % \
(expvol_fn, expvol_fn, oneDtfn)
infix2val = {'-surf_A pial':1,
'-surf_A smoothwm':2,
'-surf_A smoothwm -surf_B pial -f_steps 20': 4}
volfns = []
for hemi in hemis:
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
for infix, val in infix2val.iteritems():
fnprefix = '__m%d_%sh' % (val, hemi)
cmd = s2v_cmd % (val, specfn, infix, fnprefix)
utils.run_cmds('cd %s;%s' % (refdir, cmd))
tmpfns.extend(['%s%s' % (fnprefix, e) for e in volexts])
volfns.append(fnprefix + volor)
cmds = ['cd %s' % refdir]
catfn = '__cat'
cmds.extend(['3dTcat -overwrite -prefix %s %s' % (catfn, ' '.join(volfns)),
'3dTstat -overwrite -sum -prefix %s %s%s' % (sumfn, catfn, volor)])
tmpfns.extend(['%s%s' % (catfn, e) for e in volexts])
cmds.extend('rm %s' % fn for fn in tmpfns)
cmds.append('echo "Surface mask in %s"' % sumfn)
utils.run_cmds(';'.join(cmds), env)
# make plot
if overwrite or not os.path.exists(qafn_path):
expvol_path = '%s/%s' % (refdir, expvol_fn)
_make_slice_plot(expvol_path,
sumfn_path,
qafn_path)
def compute_fwhm(config):
# helper function - called by critical_clustersize
# computes FWHM of residuals of input data and stores in config
output_dir = c['output_dir']
is_surf = _is_surf(config)
ext, ext1D = _ext(config), _ext(config, for1D=True)
if not os.path.exists(output_dir):
os.mkdir(output_dir)
cmds = ['cd "%s"' % output_dir]
# if surfaces and needs padding, do that first
pad_to_node = config['pad_to_node']
if is_surf and pad_to_node:
data_files = []
for i, fn in enumerate(c['data_files']):
fn_pad = 'pad_%d%s' % (i, ext)
cmds.append("; ConvertDset -overwrite -pad_to_node %d -input %s'[%d]' -prefix ./%s" %
(pad_to_node, fn, config['brik_index'], fn_pad))
data_files.append(fn_pad)
pad_files = data_files
brik_index = 0
else:
data_files = c['data_files']
pad_files = []
brik_index = c['brik_index']
# bucket data from all participants into a single file
buck_fn = _fn(config, 'buck')
cmds.append('; 3dbucket -overwrite -prefix %s' % buck_fn)
for fn in data_files:
cmds.append(" %s'[%d]'" % (fn, brik_index))
# also store as 1D (won't hurt)
if is_surf:
buck_fn_1D = _fn(config, 'buck', ext1D)
cmds.append('; ConvertDset -overwrite -o_1D -prefix %s -input %s' %
(buck_fn_1D, buck_fn))
else:
buck_fn_1D = buck_fn
# compute group mean
mean_fn = _fn(config, 'mean')
cmds.append('; 3dTstat -overwrite -prefix %s %s' % (mean_fn, buck_fn))
# compute residuals, and estimate FWHM for each of them
# store FWHM output in fwhm_fn
fwhm_fn = pathjoin(output_dir, _fn(config, 'fwhm', '.1D'))
cmds.append('; echo > "%s"' % fwhm_fn)
resid_fns = []
for i in range(len(c['data_files'])):
fn = _fn(config, 'resid_%d' % i)
cmds.append("; 3dcalc -overwrite -prefix %s -a %s -b %s'[%d]' -expr 'a-b'"
% (fn, mean_fn, buck_fn, i))
msk = _mask_expr(config)
if is_surf:
surf_fn = c['surface_file']
cmds.append("; SurfFWHM %s -input %s -i_fs %s"
"| grep ^FWHM | cut -f2 -d'=' >> '%s'" %
(msk, fn, surf_fn, fwhm_fn))
else:
cmds.append('; 3dFWHMx %s %s | cut -c18- >> %s' % (msk, fn, fwhm_fn))
resid_fns.append(fn)
cmd = ''.join(cmds)
utils.run_cmds(cmd)
# read FWHM values and store in config
with open(fwhm_fn) as f:
fwhms = f.read().split()
print(fwhms)
print(fwhm_fn)
config['all_fwhms'] = fwhms # all FWHMs (for each participant)
config['fwhm'] = sum(map(float, fwhms)) / len(fwhms) # average FWHM
config['buck_fn'] = buck_fn
config['buck_fn_1D'] = buck_fn_1D
mean_fwhm_fn = pathjoin(output_dir, _fn(config, 'mean_fwhm', '.1D'))
with open(mean_fwhm_fn, 'w') as f:
f.write('%.3f\n' % config['fwhm'])
tmpfns = resid_fns + pad_files + [mean_fn]
print("TEMP")
print(tmpfns)
_remove_files(config, tmpfns)
def null_clustersize(config):
# helper function - called by critical_clustersize
# computes maxmimum cluster size of a single null permutation
output_dir = config['output_dir']
tthr = config['tthr']
fwhm = config['fwhm']
buck_fn_1D = config['buck_fn_1D']
msk = _mask_expr(config)
is_surf = _is_surf(config)
if is_surf:
surf_fn = config['surface_file']
ext, ext1D = _ext(config), _ext(config, for1D=True)
ns = len(config['data_files'])
cmds = ['cd "%s"' % output_dir]
# generate N random data files (N=number of participants)
# use the output bucket to get datasets with the right size
null_fns = []
for i in xrange(ns):
fn = _fn(config, 'rand_%d' % i, ext1D)
if is_surf:
cmds.append("; 1deval -ok_1D_text -a %s'[0]' -expr 'gran(0,1)' > '%s'" % (buck_fn_1D, fn))
else:
cmds.append("; 3dcalc -overwrite -prefix %s -a %s'[0]' -expr 'gran(0,1)'" % (fn, buck_fn_1D))
null_fns.append(fn)
# bucket random data
buck_fn = _fn(config, 'rand_buck', ext1D)
null_fns_list = ' '.join(null_fns)
if is_surf:
cmds.append('; 1dcat %s > "%s"' % (null_fns_list, buck_fn))
else:
cmds.append('; 3dbucket -overwrite -prefix %s %s' % (buck_fn, null_fns_list))
# smooth all data at once, using estimated FWHM
smooth_fn = _fn(config, 'rand_buck_smooth', ext1D)
if is_surf:
if config['sigma'] > 0:
sigma_str = '-sigma %s' % config['sigma']
else:
sigma_str = ''
cmds.append('; SurfSmooth -overwrite %s -met HEAT_07 -i_fs %s -input %s '
' -fwhm %f -output %s %s' % (msk, surf_fn, buck_fn, fwhm, smooth_fn, sigma_str))
else:
cmds.append('; 3dBlurInMask -overwrite %s -FWHM %f -prefix %s -input %s' %
(msk, fwhm, smooth_fn, buck_fn))
# run ttest
if is_surf:
msk = '' # cannot use mask on surface, but that's fine
# as it was used in SurfSmooth
ttest_fn = _fn(config, 'rand_buck_smooth_t', ext1D)
cmds.append('; 3dttest++ %s -overwrite -prefix %s -setA %s' %
(msk, ttest_fn, smooth_fn))
# extract maximum cluster size (in mm^2 or number of voxels) from output
# and pipe into size_fn
size_fn = _fn(config, 'rand_size', '.1D')
if is_surf:
postfix = "| grep --invert-match '#' | head -1 | cut -c 18-28"
cmds.append('; SurfClust -i_fs %s -input %s 1 -rmm -1 '
' -thresh %f -thresh_col 1 %s > "%s"' %
(surf_fn, ttest_fn, tthr, postfix, size_fn))
else:
postfix = " | grep --invert-match '#' | head -1 | cut -c1-8"
cmds.append("; 3dclust -quiet -1noneg -1clip %f 0 0 %s'[1]' %s > '%s'" %
(tthr, ttest_fn, postfix, size_fn))
utils.run_cmds(''.join(cmds))
# read maximum cluster size form size_fn
sz_str = None
with open(pathjoin(output_dir, size_fn)) as f:
sz_str = f.read()
try:
sz = float(sz_str)
except:
sz = 0. # CHECKME whether this makes sense
print "Null data: maximum size %f" % sz
if is_surf:
smoothing_fn_rec = pathjoin(output_dir, _fn(config, 'rand_buck_smooth', '.1D.dset.1D.smrec'))
if not os.path.exists(smoothing_fn_rec):
raise ValueError("Smoothing did not succeed. Please check the error"
" messaged. You may have to set sigma manually")
with open(smoothing_fn_rec) as f:
s = f.read()
final_fwhm = float(s.split()[-2])
ratio = fwhm / final_fwhm
thr = 0.9
if ratio < thr or 1. / ratio < thr:
raise ValueError('FWHM converged to %s but expected %s. Consider '
'setting sigma manually' % (final_fwhm, fwhm))
# clean up - remove all temporary files
tmpfns = null_fns + [buck_fn, smooth_fn, ttest_fn, size_fn]
_remove_files(config, tmpfns)
return sz
