diff --git a/cortex/brainctm.py b/cortex/brainctm.py index c242b1406..3fdea7097 100644 --- a/cortex/brainctm.py +++ b/cortex/brainctm.py @@ -89,6 +89,17 @@ def addCurvature(self, **kwargs): self.left.aux[:,1] = npz.left self.right.aux[:,1] = npz.right + def addMNI(self, **kwargs): + print('Adding MNI coords...') + npz = db.get_surfinfo(self.subject, type='mni_nl', **kwargs) + try: + self.left.mni[:,:-1] = npz.left.T + self.right.mni[:,:-1] = npz.right.T + except AttributeError: + self.left.mni = [] + self.right.mni = [] + + def save(self, path, method='mg2', disp_layers=['rois'], extra_disp=None, **kwargs): """Save CTM file for static html display. @@ -177,6 +188,7 @@ def __init__(self, pts, polys, norms=None): self.flat = None self.surfs = {} self.aux = np.zeros((len(self.ctm), 4)) + self.mni = np.zeros((len(self.ctm), 4)) def addSurf(self, pts, name=None, renorm=True): '''Scales the in-between surfaces to be same scale as fiducial''' @@ -199,6 +211,7 @@ def setFlat(self, pts): def save(self, **kwargs): self.ctm.addAttrib(self.aux, 'auxdat') + self.ctm.addAttrib(self.mni, 'mnicoords') self.ctm.save(**kwargs) ctm = CTMfile(self.tf.name) @@ -231,6 +244,7 @@ def __init__(self, pts, polys, fpolys, pia=None): self.aux[idxmap[mwidx], 0] = 1 self.mask = mask self.idxmap = idxmap + self.mni = np.zeros((len(self.ctm), 4)) def setFlat(self, pts): super(DecimatedHemi, self).setFlat(pts[self.mask]) @@ -244,6 +258,7 @@ def make_pack(outfile, subj, types=("inflated",), method='raw', level=0, ctm = BrainCTM(subj, decimate=decimate) ctm.addCurvature() + ctm.addMNI() for name in types: ctm.addSurf(name) @@ -275,5 +290,4 @@ def read_pack(ctmfile): ctm = CTMfile(tf.name, "r") pts, polys, norms = ctm.getMesh() meshes.append((pts, polys)) - return meshes diff --git a/cortex/defaults.cfg b/cortex/defaults.cfg index f0d4aa0db..75c94e9f1 100644 --- a/cortex/defaults.cfg +++ b/cortex/defaults.cfg @@ -2,6 +2,7 @@ default_cmap = RdBu_r default_cmap2D = RdBu_covar fsl_prefix = fsl5.0- +fsl_dir = 'usr/local/fsl' [mayavi_aligner] line_width = 1 diff --git a/cortex/surfinfo.py b/cortex/surfinfo.py index cb9ffca95..04c66a7ec 100644 --- a/cortex/surfinfo.py +++ b/cortex/surfinfo.py @@ -153,3 +153,177 @@ def make_surface_graph(tris): lines.append(pts[pbnd,:2]) np.savez(outfile, lines=lines, ismwalls=ismwalls) + +def mni_nl(outfile, subject, do=True, standardfile='', projection="lanczos"): + """Create an automatic alignment of an anatomical image to the MNI standard. + + This function does the following: + 1) Re-orders orientation labels on anatomical images using fslreorient2std (without modifying the existing files) + 2) Calls FLIRT + 3) Calls FNIRT with the transform estimated by FLIRT as the specified + 4) Gets the resulting warp field, samples it at each vertex location, and calculates MNI coordinates. + 5) Saves these coordinates as a surfinfo file in the db. + + Parameters + ---------- + subject : str + Subject identifier. + do : bool + Actually execute the commands (True), or just print them (False, useful for debugging). + """ + + import nibabel as nib + + from .options import config + from .dataset import Volume + + fsl_prefix = config.get("basic", "fsl_prefix") + cache = tempfile.mkdtemp() + + print('anat_to_mni, subject: %s' % subject) + resp = raw_input("This function can take up to two hours to run. Is that okay? [y/n]") + if resp == "y": + raw_anat = db.get_anat(subject, type='raw').get_filename() + bet_anat = db.get_anat(subject, type='brainmask').get_filename() + betmask_anat = db.get_anat(subject, type='brainmask_mask').get_filename() + anat_dir = os.path.dirname(raw_anat) + odir = cache + ext = '.nii.gz' + + if standardfile == '': #user did not specify the standard file, so we will try to determine... + fsl_dir = config.get("basic", "fsl_dir") + if not os.path.isdir(fsl_dir): + if 'FSLDIR' in os.environ.keys() and os.path.isdir(os.environ['FSLDIR']): + fsl_dir = os.environ['FSLDIR'] + else: # no (valid) FSLDIR env var and the config var is missing + print('Could not find FSL directory. Either specify the standard you wish to use, set the fsl_dir config variable, or set $FSLDIR...') + return + # by the time we get here, we know fsl_dir is a directory. + standard = os.path.join(fsl_dir,'data','standard', 'MNI152_T1_1mm') + else: + standard = standardfile + + if not os.path.isfile(standard) and not os.path.isfile(standard+ext): # we don't know if they passed in foo.nii.gz or just foo + print('The standard {sfile} does not exist! Aborting...'.format(sfile=standard)) + return + + bet_standard = '%s_brain'%standard + standardmask = '%s_mask_dil'%bet_standard + cout = 'mni2anat' #stem of the filenames of the transform estimates + full_cout = os.path.join(odir,cout) + + # stem for the reoriented-into-MNI anatomical images (required by FLIRT/FNIRT) + reorient_anat = 'reorient_anat' + tmpfile = os.path.join(odir, reorient_anat) + tmpfile_ext = tmpfile + ext + ra_betmask = tmpfile + "_brainmask" + + # START DOING THINGS + reorient_cmd = '{fslpre}fslreorient2std {raw_anat} {outfile}'.format(fslpre=fsl_prefix,raw_anat=raw_anat, outfile=tmpfile) + print('Reorienting anatomicals using fslreorient2std, cmd like: \n%s' % reorient_cmd) + if do and sp.call(reorient_cmd, shell=True) != 0: + raise IOError('Error calling fslreorient2std on raw anatomical') + + reorient_cmd = '{fslpre}fslreorient2std {bet_anat} {outfile}_brain'.format(fslpre=fsl_prefix,bet_anat=bet_anat, outfile=tmpfile) + if do and sp.call(reorient_cmd, shell=True) != 0: + raise IOError('Error calling fslreorient2std on brain-extracted anatomical') + + reorient_cmd = '{fslpre}fslreorient2std {bet_anat} {ra_betmask}'.format(fslpre=fsl_prefix,bet_anat=betmask_anat, ra_betmask=ra_betmask) + if do and sp.call(reorient_cmd, shell=True) != 0: + raise IOError('Error calling fslreorient2std on brain-extracted mask') + + # initial affine anatomical-to-standard registration using FLIRT. required, as the output xfm is used as a start by FNIRT. + flirt_cmd = '{fslpre}flirt -in {bet_standard} -ref {outfile}_brain -dof 6 -omat {full_cout}_flirt' + flirt_cmd = flirt_cmd.format(fslpre=fsl_prefix, bet_standard=bet_standard, outfile=tmpfile, full_cout=full_cout) + print('Running FLIRT to estimate initial affine transform with command:\n%s'%flirt_cmd) + if do and sp.call(flirt_cmd, shell=True) != 0: + raise IOError('Error calling FLIRT with command: %s' % flirt_cmd) + + # FNIRT mni-to-anat transform estimation cmd (does not apply any transform, but generates estimate [cout]) + # the MNI152 2mm config is used even though we're referencing 1mm, per this FSL list post: + # https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=FSL;d14e5a9d.1105 + cmd = '{fslpre}fnirt --in={standard} --ref={outfile} --refmask={ra_betmask} --aff={full_cout}_flirt --cout={full_cout}_fnirt --fout={full_cout}_field --iout={full_cout}_iout --config=T1_2_MNI152_2mm' + cmd = cmd.format(fslpre=fsl_prefix, outfile=tmpfile, standard=standard, ra_betmask=ra_betmask, full_cout=full_cout) + print('Running FNIRT to estimate transform, using the following command... this can take a while:\n%s'%cmd) + if do and sp.call(cmd, shell=True) != 0: + raise IOError('Error calling fnirt with cmd: %s'%cmd) + + pts, polys = db.get_surf(subject,"fiducial",merge="True") + + #print('raw anatomical: %s\nbet anatomical: %s\nflirt cmd:%s\nfnirt cmd: %s\npts: %s' % (raw_anat,bet_anat,flirt_cmd,cmd,pts)) + + # take the reoriented anatomical, get its affine coord transform, invert this, and save it + reo_xfmnm = 'reorient_inv' + # need to change this line, as the reoriented anatomical is not in the db but in /tmp now + # re_anat = db.get_anat(subject,reorient_anat) + # since the reoriented anatomicals aren't stored in the db anymore, db.get_anat() will not work (?) + re_anat = nib.load(tmpfile_ext) # remember, we set tmpfile to be the full path to the reoriented anat (and tmpfile_ext to that+.nii.gz) + reo_xfm = Transform(np.linalg.inv(re_anat.get_affine()),re_anat) + reo_xfm.save(subject,reo_xfmnm,"coord") + + # get the reoriented anatomical's qform and its inverse, they will be needed later + aqf = re_anat.get_qform() + aqfinv = np.linalg.inv(aqf) + + # load the warp field data as a volume + # since it's not in the db anymore but in /tmp instead of: + # warp = db.get_anat(subject,'%s_field'%cout) + # it's this: + warp_fn = '{full_cout}_field.nii.gz'.format(full_cout=full_cout) + # print warp_fn + warp = nib.load(warp_fn) + wd = warp.get_data() + # need in (t,z,y,x) order + wd = wd.T + wv = Volume(wd,subject,reo_xfmnm) + # need to delete the reo_xfm + reoxfmpath = os.path.split(reo_xfm.reference.get_filename())[0] + print reoxfmpath + + # now do the mapping! this gets the warp field values at the corresponding points + # (uses fiducial surface by default) + warpvd = wv.map(projection) # passed in via kwargs, defaults to lanczos + + # reshape into something sensible + warpverts_L = [vs for vs in np.swapaxes(warpvd.left,0,1)] + warpverts_R = [vs for vs in np.swapaxes(warpvd.right,0,1)] + warpverts_ordered = np.concatenate((warpverts_L, warpverts_R)) + + # append 1s for matrix multiplication (coordinate transformation) + o = np.ones((len(pts),1)) + pad_pts = np.append(pts, o, axis=1) + + # print pts, len(pts), len(pts[0]), warpverts_ordered, len(warpverts_ordered), pad_pts, len(pad_pts), pad_pts[0] + + # transform vertex coords from mm to vox using the anat's qform + voxcoords = [aqfinv.dot(padpt) for padpt in pad_pts] + # add the offsets specified in the warp at those locations (ignoring the 1s here) + mnivoxcoords = [voxcoords[n][:-1] + warpverts_ordered[n] for n in range(len(voxcoords))] + # re-pad for matrix multiplication + pad_mnivox = np.append(mnivoxcoords, o, axis=1) + + # multiply by the standard's qform to recover mm coords + + if not os.path.splitext(standard)[1]: #will be True iff no extension specified in standard file name + std = nib.load('%s.nii.gz'%standard) + else: + std = nib.load(standard) + stdqf = std.get_qform() + mni_coords = np.array([stdqf.dot(padmni)[:-1] for padmni in pad_mnivox]) + + # some debug output + # print pts, mni_coords + # print pts[0], mni_coords[0] + # print len(pts), len(mni_coords) + # print type(pts), type(pts[0][0]), type(mni_coords) + + # now split mni_coords into left and right arrays for saving + nverts_L = len(warpverts_L) + #print nverts_L + left = mni_coords[:nverts_L] + right = mni_coords[nverts_L:] + #print len(left), len(right) + + print('Saving MNI coordinates as a surfinfo ({outfile})...'.format(outfile=outfile)) + np.savez(outfile,left=left.T,right=right.T) + diff --git a/cortex/webgl/resources/css/mriview.css b/cortex/webgl/resources/css/mriview.css index 826147f4b..90ee6e539 100644 --- a/cortex/webgl/resources/css/mriview.css +++ b/cortex/webgl/resources/css/mriview.css @@ -136,6 +136,36 @@ a:visited { color:white; } background:rgba(255,255,255,.4); font-weight:bold; } + +/***** MNI Coordinate box, top left, below dataname *********/ +#mnibox { + display:none; + position:absolute; + z-index:12; + float:left; + text-shadow:0px 2px 8px black, 0px 1px 8px black; + color:white; + font-size:12pt; + padding:10px; + margin:20px; + margin-top: 80px ; + border-radius:10px; + background:rgba(255,255,255,.4); + font-weight:bold; +} + +#mnibox input.mniinput { + /*border: 0;*/ + font-size: 10pt; + font-weight: bold ; + width: 70px ; + margin-right: 5px ; +} + +#mnicoords, #mnisubmit { + z-index:13; +} + .datadesc { font-size:10pt; font-weight:normal; diff --git a/cortex/webgl/resources/js/dataset.js b/cortex/webgl/resources/js/dataset.js index 45ffa14aa..b7c64e141 100644 --- a/cortex/webgl/resources/js/dataset.js +++ b/cortex/webgl/resources/js/dataset.js @@ -247,7 +247,7 @@ var dataset = (function(module) { volxfm: { type:'m4', value: new THREE.Matrix4() }, data: { type: 't', value: 0, texture: null }, }, - attributes: { flatpos: true, wm:true, auxdat:true, }, + attributes: { flatpos: true, wm:true, auxdat:true, mnicoords:true}, }), targets = { left: new THREE.WebGLRenderTarget(res, res, { @@ -262,7 +262,7 @@ var dataset = (function(module) { }), } var hemi, geom, target, mesh, name, attr; - var names = ["position", "wm", "auxdat", "index"]; + var names = ["position", "wm", "auxdat", "index", "mnicoords"]; var limits = {top:-1000, bottom:1000}; var xfm = shader.uniforms.volxfm.value; xfm.set.apply(xfm, this.xfm); diff --git a/cortex/webgl/resources/js/facepick.js b/cortex/webgl/resources/js/facepick.js index 6df798239..ead1a9731 100644 --- a/cortex/webgl/resources/js/facepick.js +++ b/cortex/webgl/resources/js/facepick.js @@ -7,11 +7,14 @@ function FacePick(viewer, left, right) { return Math.sqrt((a[0]-b[0])*(a[0]-b[0]) + (a[1]-b[1])*(a[1]-b[1]) + (a[2]-b[2])*(a[2]-b[2])); } kdt = new kdTree([], dist, [0, 1, 2]); + mni_kdt = new kdTree([], dist, [0, 1, 2]); kdt.root = e.data.kdt; + mni_kdt.root = e.data.mnikdt; this[e.data.name] = kdt; + this['mni_' + e.data.name] = mni_kdt; }.bind(this)); - worker.postMessage({pos:left, name:"lkdt"}); - worker.postMessage({pos:right, name:"rkdt"}); + worker.postMessage({pos:left, name:"lkdt", mni:this.viewer.meshes.left.geometry.attributes.mnicoords.array}); + worker.postMessage({pos:right, name:"rkdt", mni:this.viewer.meshes.right.geometry.attributes.mnicoords.array}); this.axes = []; @@ -157,7 +160,36 @@ FacePick.prototype = { if (p) { var vec = this.viewer.uniforms.volxfm.value[0].multiplyVector3(p.pos.clone()); console.log("Picked vertex "+p.ptidx+" in "+p.hemi+" hemisphere, distance="+p.dist+", voxel=["+vec.x+","+vec.y+","+vec.z+"]"); + if (p.hemi==="left") + hem = this.viewer.meshes.left.geometry ; + if (p.hemi==="right") + hem = this.viewer.meshes.right.geometry ; + + space = $(this.viewer.object).find(".radio:checked").val(); + if (space==="magnet") { + mnix = vec.x ; + mniy = vec.y ; + mniz = vec.z ; + $(this.viewer.object).find("#coordsys_mag").prop('checked',true) ; + $(this.viewer.object).find(".units").text("vox"); + } + else { //mni or undefined + coordarray = hem.attributes.mnicoords ; + mniidx = (p.ptidx)*coordarray.itemSize ; + mnix = coordarray.array[mniidx] ; + mniy = coordarray.array[mniidx+1] ; + mniz = coordarray.array[mniidx+2] ; + $(this.viewer.object).find("#coordsys_mni").prop('checked',true) ; + $(this.viewer.object).find(".units").text("mm"); + } + this.addMarker(p.hemi, p.ptidx, keep); + $(this.viewer.object).find("#mnibox").show() ; + $(this.viewer.object).find("#mniX").val(mnix.toFixed(2)) ; + $(this.viewer.object).find("#mniY").val(mniy.toFixed(2)) ; + $(this.viewer.object).find("#mniZ").val(mniz.toFixed(2)) ; + $(this.viewer.object).find("#ptidx").val(p.ptidx) ; + $(this.viewer.object).find("#pthem").val(p.hemi) ; this.viewer.figure.notify("pick", this, [vec]); if (this.callback !== undefined) this.callback(vec, p.hemi, p.ptidx); @@ -166,6 +198,7 @@ FacePick.prototype = { this.axes[i].obj.parent.remove(this.axes[i].obj); } this.axes = []; + $(this.viewer.object).find("#mnibox").hide() ; this.viewer.schedule(); } }, @@ -281,6 +314,7 @@ FacePick.prototype = { }, addMarker: function(hemi, ptidx, keep) { + console.log('add marker: '+hemi+' idx: '+ptidx) ; var vert = this._getPos(hemi, ptidx); for (var i = 0; i < this.axes.length; i++) { if (keep === true) { diff --git a/cortex/webgl/resources/js/facepick_worker.js b/cortex/webgl/resources/js/facepick_worker.js index 47c3142b9..a13bd98c4 100644 --- a/cortex/webgl/resources/js/facepick_worker.js +++ b/cortex/webgl/resources/js/facepick_worker.js @@ -3,15 +3,18 @@ importScripts( "kdTree-min.js" ); var num = 0; self.onmessage = function( event ) { var pts = []; + var mnipts = []; for (var i = 0, il = event.data.pos.length; i < il; i+= 3) pts.push([event.data.pos[i], event.data.pos[i+1], event.data.pos[i+2], i/3]); - + for (var i = 0, il = event.data.mni.length; i < il; i+= 4) + mnipts.push([event.data.mni[i], event.data.mni[i+1], event.data.mni[i+2], i/4]) var dist = function (a, b) { return Math.sqrt((a[0]-b[0])*(a[0]-b[0]) + (a[1]-b[1])*(a[1]-b[1]) + (a[2]-b[2])*(a[2]-b[2])); } var kdt = new kdTree(pts, dist, [0, 1, 2]); + var mnikdt = new kdTree(mnipts, dist, [0, 1, 2]); - self.postMessage( {kdt:kdt.root, name:event.data.name} ); + self.postMessage( {kdt:kdt.root, name:event.data.name, mnikdt:mnikdt.root} ); if (++num > 1) self.close(); } diff --git a/cortex/webgl/resources/js/mriview.js b/cortex/webgl/resources/js/mriview.js index a12b4f5b0..b61460588 100644 --- a/cortex/webgl/resources/js/mriview.js +++ b/cortex/webgl/resources/js/mriview.js @@ -1103,6 +1103,112 @@ var mriview = (function(module) { }.bind(this)); } + //this fires when the radio button for selecting coord systems is changed + $(this.object).find(".radio").change(function() { //the .radio class is specifically for coord space selection, not all radio buttons + space = $(this.object).find(".radio:checked").val(); + ptidx = $(this.object).find("#ptidx").val(); + pthem = $(this.object).find("#pthem").val(); + if (pthem==="left") + h = this.meshes.left.geometry ; + else if (pthem==="right") + h = this.meshes.right.geometry ; + + if (typeof h !== 'undefined') { + if (space==="magnet") { + coordarray = h.attributes.position ; + $(this.object).find("#coordsys_mag").prop('checked',true) ; + mniidx = (ptidx)*coordarray.itemSize ; + px = coordarray.array[mniidx] ; + py = coordarray.array[mniidx+1] ; + pz = coordarray.array[mniidx+2] ; + console.log('mm coords: '+px+', '+py+', '+pz) ; + var coord = new THREE.Vector3(px, py, pz); + var vec = this.uniforms.volxfm.value[0].multiplyVector3(coord); + mnix = vec.x ; + mniy = vec.y ; + mniz = vec.z ; + $(this.object).find(".units").text("vox"); + } + else { //mni or undefined + coordarray = h.attributes.mnicoords ; + $(this.object).find("#coordsys_mni").prop('checked',true) ; + mniidx = (ptidx)*coordarray.itemSize ; + mnix = coordarray.array[mniidx] ; + mniy = coordarray.array[mniidx+1] ; + mniz = coordarray.array[mniidx+2] ; + $(this.object).find(".units").text("mm"); + } + $(this.object).find("#mniX").val(mnix.toFixed(2)) ; + $(this.object).find("#mniY").val(mniy.toFixed(2)) ; + $(this.object).find("#mniZ").val(mniz.toFixed(2)) ; + } + }.bind(this)); + + //this fires when the coordinate entry form is submitted -- it's time to look up the nearest vertex + $(this.object).find("#mniform").submit(function() { + x = $(this.object).find("#mniX").val(); + y = $(this.object).find("#mniY").val(); + z = $(this.object).find("#mniZ").val(); + space = $(this.object).find(".radio:checked").val(); + if (space==="magnet") { + //do some conversions to eventually get mm coords, which are what's stored in the kdtree + var coord = new THREE.Vector3(x, y, z); + var xfm = this.uniforms.volxfm.value[0] ; + var xfm_inv = new THREE.Matrix4() ; + xfm_inv = xfm_inv.getInverse(xfm); + xfm_inv.multiplyVector3(coord) ; + var left = this.picker.lkdt.nearest([coord.x, coord.y, coord.z], 1)[0]; + var right = this.picker.rkdt.nearest([coord.x, coord.y, coord.z], 1)[0]; + } + else { //mni or undefined + var left = this.picker.mni_lkdt.nearest([x, y, z], 1)[0]; + var right = this.picker.mni_rkdt.nearest([x, y, z], 1)[0]; + } + + if (left[1] < right[1]) { + ptidx = left[0][3] ; + h = this.meshes.left.geometry ; + hemi = "left" ; + } + else { + ptidx = right[0][3] ; + h = this.meshes.right.geometry ; + hemi = "right" ; + } + + this.picker.addMarker(hemi, ptidx, false); + + if (space==="magnet") + coordarray = h.attributes.position ; + else //mni or undefined + coordarray = h.attributes.mnicoords ; + + mniidx = (ptidx)*coordarray.itemSize ; + mnix = coordarray.array[mniidx] ; + mniy = coordarray.array[mniidx+1] ; + mniz = coordarray.array[mniidx+2] ; + + //if we're in MNI space, we can just update the box with the coords. if not though, we need to get vox (not mm) coords... + if (space==="magnet") { + var coord2 = new THREE.Vector3(mnix, mniy, mniz); + var vec2 = this.uniforms.volxfm.value[0].multiplyVector3(coord2); + mnix = vec2.x ; + mniy = vec2.y ; + mniz = vec2.z ; + } + + //update the hidden fields ptidx and pthem with the picked vertex's info + $(this.object).find("#ptidx").val(ptidx) ; + $(this.object).find("#pthem").val(hemi) ; + + //update coords + $(this.object).find("#mniX").val(mnix.toFixed(2)) ; + $(this.object).find("#mniY").val(mniy.toFixed(2)) ; + $(this.object).find("#mniZ").val(mniz.toFixed(2)) ; + return(0); //do not reload page + }.bind(this)); + + // Setup controls for multiple overlays var updateOverlays = function() { this.roipack.update(this.renderer).done(function(tex){ diff --git a/cortex/webgl/template.html b/cortex/webgl/template.html index 797f0dd11..d1fba00a0 100644 --- a/cortex/webgl/template.html +++ b/cortex/webgl/template.html @@ -286,6 +286,24 @@
Loading brain...
+ {% if coord_disp %} +
+
+ Coordinates +
+ + MNI + Magnet
 + + + X:
+ Y:
+ Z:
+ +
+
+
+ {% end %}
diff --git a/cortex/webgl/view.py b/cortex/webgl/view.py index 83db638b9..7899a2e90 100644 --- a/cortex/webgl/view.py +++ b/cortex/webgl/view.py @@ -204,7 +204,7 @@ def make_static(outpath, data, types=("inflated",), recache=False, cmap="RdBu_r" def show(data, types=("inflated",), recache=False, cmap='RdBu_r', layout=None, autoclose=True, open_browser=True, port=None, pickerfun=None, - disp_layers=['rois'], extra_disp=None, **kwargs): + disp_layers=['rois'], extra_disp=None, coord_disp=True, **kwargs): """Display a dynamic viewer using the given dataset. See cortex.webgl.make_static for help. """ data = dataset.normalize(data) @@ -314,6 +314,7 @@ def get(self): subjects=subjectjs, disp_layers=disp_layers+dl, disp_defaults=_make_disp_defaults(disp_layers+dl), + coord_disp=coord_disp, **viewopts) self.write(generated) diff --git a/docs/align.rst b/docs/align.rst index 804cd46b9..39776297b 100644 --- a/docs/align.rst +++ b/docs/align.rst @@ -1,3 +1,7 @@ Aligner ======= +This module contains functions for manual and automatic alignment of brain images and cortical surfaces. For each transform, it saves a transform matrix, which maps pixels to voxels. +The automatic() function does epi-to-anat registration using FLIRT with BBR, then inverts this with Transform.from_fsl() + +The anat_to_mni() function uses FNIRT to register the MNI surface to the subject's surface, then estimates the MNI coords corresponding to vertex coords. \ No newline at end of file diff --git a/docs/mapper.rst b/docs/mapper.rst new file mode 100644 index 000000000..b3e4f0fb5 --- /dev/null +++ b/docs/mapper.rst @@ -0,0 +1,5 @@ +Mapper +====== +This module contains functions and classes that translate between Volumes of data and the corresponding Vertices of a surface using any of several samplers. That is, if you have some data defined on a per-voxel basis (whether it's BOLD or a warp vector doesn't matter), you can create a Volume and use the map() function to sample from that data at the vertices of a surface. And you can specify the sampling method, be it nearest-neighbor, trilinear, sinc, etc... + +Important Classes: \ No newline at end of file