[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.


Sorry, of course I meant that it should NOT affect anything else.

BW,

JM

>> 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
>> 
>> 
>> 
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
> 
> 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
> 
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip

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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