You can also map the sulc or curv to fsaverage. The coordinates (in freeview or tksurfer) are in MNI305 coordinates which are pretty close to Tal.
doug On 09/28/2015 05:26 PM, Rudolph Pienaar wrote: > Hi Karen -- > > A given FreeSurfer surface can be thought of as a triangular mesh. This > mesh contains many "points" (i.e. the vertex points of the constituent > triangles). > > Each of these mesh vertex points contains many internal values, i.e. the > x, y, z position of the point, the normal to the surface at this point, > some curvature values at this point, and many more. > > Each of these mesh points is also referenced by a single number, its ID > if you will. If there are 100,000 mesh points, this ID will range in > value from 0 (the arbitrary first point) to 99,999 (the last point on > the mesh). > > A sulc or curvature file, is simply a long array of sulc or curvature > values. The index of the array corresponds to the ID of the same indexed > point on the FreeSurfer surface (there is slightly confusing change in > that in MatLAB counting of arrays starts at 1, while in FreeSurfer the > counting starts at 0). So, for example, a file "lh.sulc", is simply a > long list of values, in order, corresponding to the sulc value at each > corresponding index location of the surface. > > So, in MatLAB, a line like: > > [curv, fnum] = read_curv(fname); > > and assuming that > > fname = '/some/path/to/lh.sulc'; > > will read the lh.sulc located at the directory spec '/some/path/to/' and > will return two bits of data. The 'fnum' you can ignore. The 'curv' is > what you are interested in. It is a MatLAB array (or vector) of, in this > case, the sulc values. > > curv[1] corresponds to the sulc value at the first mesh point (which is > actually index 0 of the mesh). > > curv[2] corresponds to the sulc value at the second mesh point (which is > actually index 1 of the mesh). > > and so on and so forth. > > If you set fname to > > fname = '/some/path/to/lh.curv'; > > then the lh.curv file and its values are read and returned as the > indexed MatLAB vector. > > In order to get the sulc and curv at a given tal coordinate, you'd have > to map the tal coordinate to the index of the point on the FreeSurfer mesh. > > HTH > -=R > > On 9/28/15 12:31 , Bunday, Karen wrote: >> Hi >> >> I am not a Freesurfer expert or Matlab connoisseur. I am trying to find >> out how to get the Sulc and Curv value for a given tal coordinate. I >> was told that you load it in Matlab using read_curv, but how exactly do >> I do this, what does they syntax look like? >> >> I can see in the help this: [curv, fnum] = read_curv(fname) >> >> But I don’t know what I’m supposed to out in here more explicitly. >> >> Thanks >> >> Karen >> >> Karen Bunday, PhD >> >> Honorary Research Associate >> >> Sobell Department of Motor Neuroscience and Movement Disorders >> >> Institute of Neurology, University College London >> >> 33 Queen Square >> >> London >> >> WC1N 3BG >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it is >> addressed. If you believe this e-mail was sent to you in error and the e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you in >> error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
