[caret-users] Errors in Stage-3.FS-to-F99.sh: Expected '>' or '/', but got '[0-9]'

Donna Dierker donna at brainvis.wustl.edu
Fri Feb 28 11:32:00 CST 2014


This ended up being a well-intentioned script doing a global replacement on a coord & surface_shape file, but that replacement introduced non-integer characters into the Dim0 XML attribute.  So, if you see an error like this:

>> BrainSet construction error: Expected '>' or '/', but got '[0-9]'.

Try "grep Dim0 myfile" and make sure this attribute is set to an integer (e.g., 73730 -- not 74k_f99).


On Feb 7, 2014, at 10:07 AM, Donna Dierker <donna at brainvis.wustl.edu> wrote:

> I checked, and there was some off-list exchange between me and the poster, but it didn't address this error, per se.
> 
> The solution for this user was to use mri_convert to reorient rawavg.mgz, which was in sphinx orientation, the translate per http://brainvis.wustl.edu/pipermail/caret-users/2012-July/005618.html.
> 
> It's not at all clear to me how that relates to the scene creation errors below, but I'm summarizing the off-list exhchange.
> 
> 
> On Feb 7, 2014, at 8:23 AM, Caspar M. Schwiedrzik <cschwiedrz at mail.rockefeller.edu> wrote:
> 
>> Hi! 
>> 
>> I am running into some error messages try to align a Freesurfer surface to the F99. 
>> The errors arise in the Stage-3.FS-to-F99.sh script and have been described on the list before:
>> https://www.mail-archive.com/caret-users@brainvis.wustl.edu/msg02854.html
>> 
>> Specifically, I am getting the following messages:
>> 
>> BrainSet construction error: Expected '>' or '/', but got '[0-9]'.
>> SURFACE DISTORTION ERROR: unable to find second surface.
>> 
>> and 
>> 
>> SCENE CREATION ERROR: Expected '>' or '/', but got '[0-9]'.
>> Expected '>' or '/', but got '[0-9]'.
>> Expected '>' or '/', but got '[0-9]'.
>> 
>> Unfortunately, the previous thread did not provide a solution. 
>> Is there a known way to get around this? 
>> Thanks, Caspar




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