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_makespec_bothhemis(config, env):
refdir = config['refdir']
overwrite = config['overwrite']
icolds, hemis = _get_hemis_icolds(config)
ext = format2extension(config)
if hemis != ['l', 'r']:
raise ValueError("Cannot run without left and right hemisphere")
for icold in icolds:
specs = []
for hemi in hemis:
#surfprefix = '%s%sh' % (config['mi_icopat'] % icold, hemi)
specfn = afni_suma_spec.canonical_filename(icold, hemi,
config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
s = afni_suma_spec.read(specpathfn)
specs.append(afni_suma_spec.read(specpathfn))
add_states = ['inflated', 'full.patch.flat', 'sphere.reg']
add_states_required = [True, False, True] # flat surface is optional
for add_state, is_req in zip(add_states, add_states_required):
has_state = all([len(spec.find_surface_from_state(add_state)) == 1
for spec in specs])
if not has_state:
if is_req:
error('cannot find state %s' % add_state)
else:
# skip this state
print "Optional state %s not found - skipping" % add_state
continue
specs = afni_suma_spec.hemi_pairs_add_views(specs,
add_state, ext, refdir, overwrite=overwrite)
spec_both = afni_suma_spec.combine_left_right(specs)
# generate spec files for both hemispheres
hemiboth = 'b'
specfn = afni_suma_spec.canonical_filename(icold, hemiboth, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
spec_both.write(specpathfn, overwrite=overwrite)
# merge left and right into one surface
# and generate the spec files as well
hemimerged = 'm'
specfn = afni_suma_spec.canonical_filename(icold, hemimerged, config['alsuffix'])
specpathfn = os.path.join(refdir, specfn)
if config['overwrite'] or not os.path.exists(specpathfn):
spec_merged, surfs_to_join = afni_suma_spec.merge_left_right(spec_both)
spec_merged.write(specpathfn, overwrite=overwrite)
full_path = lambda x:os.path.join(refdir, x)
for fn_out, fns_in in surfs_to_join.iteritems():
surfs_in = [surf.read(full_path(fn)) for fn in fns_in]
if all(['full.patch.flat' in fn for fn in fns_in]):
# left hemi of flat; rotate 180 degrees, reposition again
surfs_in[0] = surfs_in[0] * [-1, -1, 1]
surfs_in = surf.reposition_hemisphere_pairs(surfs_in[0], surfs_in[1], 'm')
surf_merged = surf.merge(*surfs_in)
if config['overwrite'] or not os.path.exists(full_path(fn_out)):
surf.write(full_path(fn_out), surf_merged)
print "Merged surfaces written to %s" % fn_out
def average_fs_asc_surfs(fn1, fn2, fnout):
'''averages two surfaces'''
surf1 = surf.read(fn1)
surf2 = surf.read(fn2)
surfavg = surf1 * .5 + surf2 * .5
surf.write(fnout, surfavg)