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Bug 1888 - deployed fieldtrip crashes

Reported 2012-12-12 20:13:00 +0100
Modified 2013-05-09 08:31:47 +0200
Product: FieldTrip
Component: core
Version: unspecified
Hardware: PC
Operating System: Mac OS
Importance: P3 normal
Assigned to: Jan-Mathijs Schoffelen
Depends on:
See also:

Jan-Mathijs Schoffelen - 2012-12-12 20:13:34 +0100

when it needs to rely on templates that are not configureable, or when templates are specified from within the fieldtrip release. The latter is the cause for the former, because the defaults are always taken from ~/templates/... ~/external/spm8/template/... TODO: -identify which functions are affected: at least * ft_volumenormalise * ft_volumesegment * utilities/align_ctf2spm * utilities/align_itab2spm -make the template configureable if that's not the case yet. This is at least the case with align_xxx2yyy -build in a check in the respective functions: e.g. if isdeployed, do the check if the user has specified anything that makes sense, else, default to the template within the FT release; end

Jan-Mathijs Schoffelen - 2012-12-12 21:57:00 +0100

another candidate to consider: ft_convert_coordsys (caller function of align_xxx2spm) I implemented explicitly checking for being deployed and the requirement for a cfg.template in ft_volumesegment and ft_volumenormalise. Testing just now.

Jan-Mathijs Schoffelen - 2012-12-12 22:41:26 +0100

ft_volumerealign also needs to be adjusted when cfg.method = 'headshape'

Jan-Mathijs Schoffelen - 2012-12-18 09:42:56 +0100

bash-3.2$ svn commit ft_volumesegment.m ft_volumenormalise.m utilities/ft_convert_coordsys.m utilities/private/align_ctf2spm.m Sending ft_volumenormalise.m Sending ft_volumesegment.m Sending utilities/ft_convert_coordsys.m Sending utilities/private/align_ctf2spm.m Transmitting file data .... Committed revision 7220. bash-3.2$ svn commit ft_volumerealign.m Sending ft_volumerealign.m Transmitting file data . Committed revision 7221. TO DO: align_itab2spm.m

Jan-Mathijs Schoffelen - 2012-12-20 20:58:14 +0100

TO DO: align_itab2spm Now deployed FT also still crashes when trying to use openmeeg because it cannot seem to find the software, even though the environment variables are known within the shell from which the deployed application is started. Does this have to do with the fact that the path should be known upon compilation? And that the path cannot be changed dynamically when deployed?

Jan-Mathijs Schoffelen - 2012-12-20 20:59:04 +0100

Die verrekte anatomy pipeline laat zich maar niet deployen.

Jan-Mathijs Schoffelen - 2013-01-16 15:51:27 +0100

Problem identified: the shell-script automatically starts with an empty library path, causing all user specified settings to disappear. manually changing this in the shell script solves the issue.

Jan-Mathijs Schoffelen - 2013-05-06 20:16:37 +0200