Merge pull request gallantlab#309 from gallantlab/fsalign_manual

fsalign manual

cortex/align.py

@@ -82,6 +82,98 @@ def view_callback(aligner):
 
     return m
 
+def fs_manual(subject, xfmname, output_name="register.lta", wm_color="blue", pial_color="red", noclean=False):
+    """Open Freesurfer FreeView GUI for manually aligning/adjusting a functional
+    volume to the cortical surface for `subject`. This creates a new transform
+    called `xfmname`. The name of a nibabel-readable file (e.g. NIfTI) should be
+    supplied as `reference`. This image will be copied into the database.
+
+    IMPORTANT: This function assumes that the resulting .lta file is saved as:
+    "{default folder chosen by FreeView (should be /tmp/fsalign_xxx)}/{output_name}".
+
+    Parameters
+    ----------
+    subject : str
+        Subject identifier.
+    xfmname : str
+        The name of the transform to be modified.
+    output_name : str
+        The name of the .lta file generated after FreeView editing.
+    wm_color : str | "blue"
+        Color of the white matter surface. Default is "blue". This can
+        also be adjusted in the FreeView GUI.
+    pial_color : str | "red"
+        Color of the pial surface. Default is "red". This can also be adjusted
+        the FreeView GUI.
+    noclean : boolean | False
+        If True, intermediate files will not be removed from /tmp/fsalign_xxx
+        (this is useful for debugging things), and the returned value will be
+        the name of the temp directory. Default False.
+
+    Returns
+    -------
+    Nothing unless noclean is true.
+    """
+
+    import subprocess as sp
+    import tempfile
+    import shutil
+    from .xfm import Transform
+    from .database import db
+
+    retval = None
+
+    try:
+        try:
+            cache = tempfile.mkdtemp(prefix="fsalign_")
+            sub_xfm = db.get_xfm(subject, xfmname)
+
+            # if masks have been cached, quit! user must remove them by hand
+            from glob import glob
+            if len(glob(db.get_paths(subject)['masks'].format(xfmname=xfmname, type='*'))):
+                print('Refusing to overwrite existing transform %s because there are cached masks. Delete the masks manually if you want to modify the transform.' % xfmname)
+                raise ValueError('Exiting...')
+        except IOError:
+            print("Transform does not exist!")
+
+        # Load transform-relevant things
+        reference = sub_xfm.reference.get_filename()
+        xfm_dir = os.path.dirname(reference)
+        _ = sub_xfm.to_freesurfer(os.path.join(cache, "register.dat"), subject) # Transform in freesurfer .dat format
+
+        # Command for FreeView and run
+        cmd = ("freeview -v $SUBJECTS_DIR/{sub}/mri/orig.mgz "
+                "{ref}:reg={reg} "
+               "-f $SUBJECTS_DIR/{sub}/surf/lh.white:edgecolor={wmc} $SUBJECTS_DIR/{sub}/surf/rh.white:edgecolor={wmc} "
+               "$SUBJECTS_DIR/{sub}/surf/lh.pial:edgecolor={pialc} $SUBJECTS_DIR/{sub}/surf/rh.pial:edgecolor={pialc}")
+        cmd = cmd.format(sub=subject, ref=reference, reg=os.path.join(cache, "register.dat"),
+                         wmc=wm_color, pialc=pial_color)
+
+        # Run and save transform when user is done editing
+        if sp.call(cmd, shell=True) != 0:
+            raise IOError("Problem with FreeView!")
+        else:
+            # Convert transform into .dat format
+            reg_dat = os.path.join(cache, os.path.splitext(output_name)[0] + ".dat")
+            cmd = "lta_convert --inlta {inlta} --outreg {regdat}"
+            cmd = cmd.format(inlta=os.path.join(cache, output_name), regdat=reg_dat)
+            if sp.call(cmd, shell=True) != 0:
+                raise IOError("Error converting lta into dat!")
+
+            # Save transform to pycortex
+            xfm = Transform.from_freesurfer(reg_dat, reference, subject)
+            db.save_xfm(subject, xfmname, xfm.xfm, xfmtype='coord', reference=reference)
+            print("saved xfm")
+
+    finally:
+        if not noclean:
+            shutil.rmtree(cache)
+        else:
+            retval = cache
+
+    return retval
+
+
 def automatic(subject, xfmname, reference, noclean=False, bbrtype="signed", pre_flirt_args='', use_fs_bbr=False):
     """Create an automatic alignment using the FLIRT boundary-based alignment (BBR) from FSL.
 
@@ -113,6 +205,9 @@ def automatic(subject, xfmname, reference, noclean=False, bbrtype="signed", pre_
         Additional arguments that are passed to the FLIRT pre-alignment step (not BBR).
     use_fs_bbr : bool, optional
         If True will use freesurfer bbregister instead of FSL BBR.
+    save_dat : bool, optional
+        If True, will save the register.dat file from freesurfer bbregister into
+        freesurfer's $SUBJECTS_DIR/subject/tmp.
 
     Returns
     -------
@@ -139,6 +234,7 @@ def automatic(subject, xfmname, reference, noclean=False, bbrtype="signed", pre_
             print('Running freesurfer BBR')
             cmd = 'bbregister --s {sub} --mov {absref} --init-fsl --reg {cache}/register.dat --t1'
             cmd = cmd.format(sub=subject, absref=absreference, cache=cache)
+
             if sp.call(cmd, shell=True) != 0:
                 raise IOError('Error calling freesurfer BBR!')
 

cortex/xfm.py

@@ -211,9 +211,9 @@ def from_freesurfer(cls, fs_register, func_nii, subject, freesurfer_subject_dir=
         Parameters
         ----------
         fs_register : array
-            4x4 transformation matrix, described in an FreeSurfer register.dat file, for a transform computed
+            4x4 transformation matrix, described in an FreeSurfer .dat or .lta file, for a transform computed
             FROM the func_nii volume TO the anatomical volume of the FreeSurfer subject `subject`.
-            Alternatively, a string file name for the FreeSurfer register.dat file.
+            Alternatively, a string file name for the FreeSurfer .dat or .lta file.
         func_nii : str or nibabel.Nifti1Image
             nibabel image object (or string path to nibabel-readable image) for (functional) data volume
             to be projected onto cortical surface
@@ -246,6 +246,7 @@ def from_freesurfer(cls, fs_register, func_nii, subject, freesurfer_subject_dir=
         if isinstance(fs_register, string_types):
             with open(fs_register, 'r') as fid:
                 L = fid.readlines()
+
             anat2func = np.array([[np.float(s) for s in ll.split() if s] for ll in L[4:8]])
         else:
             anat2func = fs_register
@@ -353,7 +354,7 @@ def to_freesurfer(self, fs_register, subject, freesurfer_subject_dir=None):
         # Read tkvox2ras transform for the functional volume
         try:
             cmd = ('mri_info', '--vox2ras-tkr', func_nii)
-            L = subprocess.check_output(cmd).splitlines()
+            L = subprocess.check_output(cmd).splitlines()[1:]
             func_tkrvox2ras = np.array([[np.float(s) for s in ll.split() if s] for ll in L])
         except OSError:
             print ("Error occured while executing:\n{}".format(' '.join(cmd)))
@@ -362,7 +363,7 @@ def to_freesurfer(self, fs_register, subject, freesurfer_subject_dir=None):
         # Read voxel resolution of the functional volume
         try:
             cmd = ('mri_info', '--res', func_nii)
-            ll = subprocess.check_output(cmd)
+            ll = subprocess.check_output(cmd).split("\n")[1]
             func_voxres = np.array([np.float(s) for s in ll.split() if s])
         except OSError:
             print ("Error occured while executing:\n{}".format(' '.join(cmd)))