HI Daan

wow, that is a pretty unusual folding pattern, which I'm sure is the source of the issue. Are you sure which one is the central sulcus? If so, draw it (I guess using tksurfer as the current version of freeview doesn't have extensive surface drawing tools yet), probably by just "custom filling" the sulc, then rerun mris_register using the flag:

mris_register --help | grep "-L" Usage: grep [OPTION]... PATTERN [FILE]... Try 'grep --help' for more information. tiamat [C2.3T.recon] mris_register --help | grep "-L" -L <labelfile atlas_gcsa_file label_name>

where label_name is the exact name of the central sulcus label in the gcsa file you use, and can be obtained by looking in our color lookup table file such as FreeSurferColorLUT.txt, or just running mris_info on the gcsa file you are using (they are all in $FREESURFER_HOME/average).

cheers Bruce

On Tue, 14 Mar 2017, Daan Wesselink wrote:

Dear Douglas,

Thank you for your response. The surface placement on the individual seems correct (see https://ibb.co/f4aeAa ). However, if I load the annotation files, the labels are wrong. In this screenshot (https://ibb.co/cycFiv ), I've loaded the BA annotation outlines and BA3a in yellow on the left hemisphere. It seems to think the wrong fold is the central sulcus.

Thanks,

Daan

  Message: 7
  Date: Sun, 12 Mar 2017 19:00:21 -0400
  From: Douglas Greve <greve@nmr.mgh.harvard.edu>
  Subject: Re: [Freesurfer] Faulty alignment to standard surface
  To: freesurfer@nmr.mgh.harvard.edu
  Message-ID:
  <7ab364ef-539f-fd65-4346-db68d915ca05@nmr.mgh.harvard.edu>
  Content-Type: text/plain; charset="windows-1252"

  not sure what you mean. Can you send a pic? Is the surface
  placement on
  the individual correct (ie, are the white and pial surfaces
  properly
  placed on the T1)?


  On 3/10/17 11:19 AM, Daan Wesselink wrote:
  > Dear experts,
  >
  > I've run the standard recon-all pipeline on a subject, for
  whom the
  > log does not report any errors and the white and pial surface
  follow
  > the structural nicely. However, the coregistration to the
  standard
  > surface has gone wrong: it seems like the central sulcus (e.g.
  labels
  > BA1, BA3a) is placed on top of the postcentral sulcus.
  >
  > Does someone know how to fix this problem and/or better
  identify the
  > step where it went wrong?
  >
  > Many thanks,
  >
  > Daan Wesselink
  >
  >

...

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