[FieldTrip] FW: problem with ft_prepare_singleshell

[jan-mathijs schoffelen]

Dear Beth,

Sorry for the bug. This is indeed a known problem which has found its way into recent versions. We are working on a permanent fix. I just checked in a temporary patch which should be available for download as of tonight (CET), or can be checked out from google-code soon. Alternatively, you could replace the recent version of ft_prepare_singleshell with and old version which works for you. This should affect anything else.

Thanks for reporting this and sorry for the inconvenience.

Best wishes,

Jan-Mathijs


On Sep 16, 2011, at 11:31 PM, Belluscio, Beth (NIH/NINDS) [E] wrote:

> Hi fellow fieldtrip users-
>  I am currently using fieldtrip version 20110913 and have encountered a problem that wasn't there before.  After reslicing and segmenting my mri data (which was realigned to CTF format), I segmented the data using cfg.output = {'skullstrip' 'brain'} and seg = ft_volumesegment(cfg, mri).  I saved the resulting seg matrix. 
>  Then, when I run ft_prepare_singleshell to generate my volumetric model (vol):
> 
> cfg = [];
> vol = ft_prepare_singleshell(cfg, seg)
> 
> I get the following messages and error.
> 
> 
> 
> not downsampling anatomy
> not downsampling brain
> the call to "ft_volumedownsample" took 0 seconds and an estimated 0 MB
> using the segmentation approach
> Warning: adding /home/belluscb/nindsip/matlab/fieldtrip-20110913/external/spm8 toolbox to your
> Matlab path 
> using the segmented MRI
> ??? Reference to non-existent field 'seg'.
> 
> Error in ==> prepare_mesh_segmentation at 63
> [mrix, mriy, mriz] = ndgrid(1:size(mri.seg,1), 1:size(mri.seg,2), 1:size(mri.seg,3));
> 
> Error in ==> ft_prepare_mesh at 124
>  bnd = prepare_mesh_segmentation(cfg, mri);
> 
> Error in ==> ft_prepare_singleshell at 89
>  vol.bnd = ft_prepare_mesh(cfg, mri);
> 
> 
> 
> 
> If I use an old version of fieldtrip (20100505) that I had, and run the same command cfg = [];
> vol = ft_prepare_singleshell(cfg, seg)  on the same seg matrix, it runs without a problem.  
> 
> I am not skilled enough (yet) at reading code to figure out what is not working with the recent version of fieldtrip.  
> Can someone please assist me?
> 
> Thanks!
> Beth.
> 
> 
> Beth Belluscio MD-PhD
> Clinical Fellow
> Human Motor Control Section
> NINDS, NIH
> 301-402-3495
> 
> 
> 
> _______________________________________________
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> fieldtrip at donders.ru.nl
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Jan-Mathijs Schoffelen, MD PhD 
Donders Institute for Brain, Cognition and Behaviour, 
Centre for Cognitive Neuroimaging,
Radboud University Nijmegen, The Netherlands
J.Schoffelen at donders.ru.nl
Telephone: +31-24-3614793

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