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 <gr...@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] Faulty alignment to standard surface
To: freesurfer@nmr.mgh.harvard.edu
Message-ID:
<7ab364ef-539f-fd65-4346-db68d915c...@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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