def fetch_b0_to_tkr(b0vol_fname,trk_fname,fsenvsrc=None,out_fname=None): '''automated function to generate transformation matrix from B0 volume to volume RAS coordinates. first of two automated transform generator functions and considerably simpler than the next one. if out_fname is not supplied, returns a numpy matrix containing the affine transform. Include the fsenvsrc parameter if nmrenv has not already been set.''' if fsenvsrc: import cvu_utils cvu_utils.tcsh_env_interpreter(fsenvsrc) v=1.0/read_header(trk_fname)['vox_size'] import subprocess cmd = 'mri_info %s --vox2ras-tkr' % (b0vol_fname) proc=subprocess.Popen(cmd,shell=True,stdout=subprocess.PIPE) crs_to_tkr_arr=np.loadtxt(proc.stdout) b0_to_crs_arr=np.diag((v,v,v,1)) ret = np.dot(b0_to_crs_arr,crs_to_tkr_arr) if out_fname: np.savetxt(out_fname,ret) else: return ret
def fetch_b0_to_tkr(b0vol_fname, trk_fname, fsenvsrc=None, out_fname=None):
'''automated function to generate transformation matrix from B0 volume
to volume RAS coordinates. first of two automated transform generator
functions and considerably simpler than the next one. if out_fname is not
supplied, returns a numpy matrix containing the affine transform.
Include the fsenvsrc parameter if nmrenv has not already been set.'''
if fsenvsrc:
import cvu_utils
cvu_utils.tcsh_env_interpreter(fsenvsrc)
v = 1.0 / read_header(trk_fname)['vox_size']
import subprocess
cmd = 'mri_info %s --vox2ras-tkr' % (b0vol_fname)
proc = subprocess.Popen(cmd, shell=True, stdout=subprocess.PIPE)
crs_to_tkr_arr = np.loadtxt(proc.stdout)
b0_to_crs_arr = np.diag((v, v, v, 1))
ret = np.dot(b0_to_crs_arr, crs_to_tkr_arr)
if out_fname:
np.savetxt(out_fname, ret)
else:
return ret
def fetch_ras_to_tkr(b0vol_fname,
fs_subj_name,
fs_subjects_dir,
fsenvsrc=None,
out_fname=None):
'''automated function to generate transformation from surface RAS to volume
RAS coordinates. bbregister is used to do this. this function takes a few minutes. if out_fname is not supplied, returns a numpy matrix containing the
affine transform.
Include the fsenvsrc if nmrenv has not already been set.'''
import subprocess
import tempfile
import glob
if fsenvsrc:
import cvu_utils
cvu_utils.tcsh_env_interpreter(fsenvsrc)
os.environ['SUBJECTS_DIR'] = fs_subjects_dir
tmpfd, tmpfname = tempfile.mkstemp()
cmd = ('bbregister --s %s --mov %s --init-fsl --reg \'%s\' --bold '
'--tol1d 1e-3' % (fs_subj_name, b0vol_fname, tmpfname + ".reg"))
#print os.environ['SUBJECTS_DIR']
#print cmd
with open(os.devnull, 'wb') as devnull:
proc = subprocess.Popen(cmd, shell=True, stdout=devnull)
if proc.wait() != 0:
for i in glob.glob('tmpfname*'):
os.unlink(i)
raise cvu_utils.CVUError("bbregister crashed with error %i" %
proc.returncode)
with open(tmpfname + '.reg', 'rwb') as tmpf:
for i in xrange(4):
tmpf.readline() #ignore first 4 lines
with os.tmpfile() as tmpf2:
for j in xrange(4):
tmpf2.write(tmpf.readline() + '\n')
tmpf2.seek(0)
ret = np.loadtxt(tmpf2)
for i in glob.glob('tmpfname*'):
os.unlink(i)
#TODO also unlink all the other things this creates in /tmp
if out_fname:
np.savetxt(out_fname, ret)
else:
return ret
def apply_affines_carefully(s, b0vol_fname, trk_fname, fs_subj_name, fs_subj_dir, fsenvsrc=None): if fsenvsrc: import cvu_utils cvu_utils.tcsh_env_interpreter(fsenvsrc) a1=fetch_b0_to_tkr(b0vol_fname,trk_fname) a2=fetch_ras_to_tkr(b0vol_fname,fs_subj_name,fs_subj_dir) a2i=reverse_affine(a2) apply_affine_carefully(a1,s) #apply_affine_inversely(a2,s) apply_affine_carefully(a2i,s) mlab.view(focalpoint='auto')
def fetch_ras_to_tkr(b0vol_fname,fs_subj_name,fs_subjects_dir,fsenvsrc=None
,out_fname=None):
'''automated function to generate transformation from surface RAS to volume
RAS coordinates. bbregister is used to do this. this function takes a few minutes. if out_fname is not supplied, returns a numpy matrix containing the
affine transform.
Include the fsenvsrc if nmrenv has not already been set.'''
import subprocess; import tempfile; import glob
if fsenvsrc:
import cvu_utils
cvu_utils.tcsh_env_interpreter(fsenvsrc)
os.environ['SUBJECTS_DIR']=fs_subjects_dir
tmpfd,tmpfname=tempfile.mkstemp()
cmd = ('bbregister --s %s --mov %s --init-fsl --reg \'%s\' --bold '
'--tol1d 1e-3' % (fs_subj_name, b0vol_fname, tmpfname+".reg"))
#print os.environ['SUBJECTS_DIR']
#print cmd
with open(os.devnull,'wb') as devnull:
proc=subprocess.Popen(cmd,shell=True,stdout=devnull)
if proc.wait() != 0:
for i in glob.glob('tmpfname*'):
os.unlink(i)
raise cvu_utils.CVUError("bbregister crashed with error %i" %
proc.returncode)
with open(tmpfname+'.reg','rwb') as tmpf:
for i in xrange(4):
tmpf.readline() #ignore first 4 lines
with os.tmpfile() as tmpf2:
for j in xrange(4):
tmpf2.write(tmpf.readline()+'\n')
tmpf2.seek(0)
ret = np.loadtxt(tmpf2)
for i in glob.glob('tmpfname*'):
os.unlink(i)
#TODO also unlink all the other things this creates in /tmp
if out_fname:
np.savetxt(out_fname,ret)
else:
return ret
def apply_affines_carefully(s,
b0vol_fname,
trk_fname,
fs_subj_name,
fs_subj_dir,
fsenvsrc=None):
if fsenvsrc:
import cvu_utils
cvu_utils.tcsh_env_interpreter(fsenvsrc)
a1 = fetch_b0_to_tkr(b0vol_fname, trk_fname)
a2 = fetch_ras_to_tkr(b0vol_fname, fs_subj_name, fs_subj_dir)
a2i = reverse_affine(a2)
apply_affine_carefully(a1, s)
#apply_affine_inversely(a2,s)
apply_affine_carefully(a2i, s)
mlab.view(focalpoint='auto')
def apply_cmp_affines(s,b0vol_fname,trk_fname,fs_subj_name, fs_subjs_dir,fsenvsrc=None): '''applies B0-TKR transform and then TKR-RAS transform Include the fsenvsrc parameter if nmrenv has not already been set''' if fsenvsrc: import cvu_utils cvu_utils.tcsh_env_interpreter(fsenvsrc) a1=fetch_b0_to_tkr(b0vol_fname,trk_fname) a2=fetch_ras_to_tkr(b0vol_fname,fs_subj_name,fs_subjs_dir) a2i=reverse_affine(a2) co=np.dot(a1,a2) #compose these transformations apply_affine(co,s) mlab.view(focalpoint='auto')
def apply_cmp_affines(s,
b0vol_fname,
trk_fname,
fs_subj_name,
fs_subjs_dir,
fsenvsrc=None):
'''applies B0-TKR transform and then TKR-RAS transform
Include the fsenvsrc parameter if nmrenv has not already been set'''
if fsenvsrc:
import cvu_utils
cvu_utils.tcsh_env_interpreter(fsenvsrc)
a1 = fetch_b0_to_tkr(b0vol_fname, trk_fname)
a2 = fetch_ras_to_tkr(b0vol_fname, fs_subj_name, fs_subjs_dir)
a2i = reverse_affine(a2)
co = np.dot(a1, a2) #compose these transformations
apply_affine(co, s)
mlab.view(focalpoint='auto')
