prepare_single_shell errors

[Sameer Walawalkar]

Hi,

I am trying to use prepare_singleshell to try and get a single shell model
using brain surface from segmented mri.

I try to generate this segmented mri using (is this correct)

>> [mri]=
read_fcdc_mri('/mnt/condor2/sameer/Software/freesurfer/subjects/WS/mri/T1-neuromag/sets/COR.fif')

mri =

           dim: [256 256 256]
       anatomy: [256x256x256 uint8]
           hdr: [1x1 struct]
     transform: [4x4 double]

The file COR.fif is acquired by implementing  mne_setup_mri of MNE-suite,
and it in turn acts upon freeserfer treatment of dicom files of mri data.

Then,
>> cfg = [];   cfg.gradfile = 'ws_011207_1_checkers.fif';
>> ft_singleshell = prepare_singleshell(cfg,mri);
smoothing the segmentation with a 5-pixel FWHM kernel
Warning: Divide by zero.
> In mean at 29
   In prepare_singleshell at 100
Warning: Divide by zero.
> In mean at 29
   In prepare_singleshell at 101
Warning: Divide by zero.
> In mean at 29
   In prepare_singleshell at 102
??? Subscript indices must either be real positive integers or logicals.

Error in ==> fieldtrip/private/triangulate_seg at 55
   int = seg(sel);

Error in ==> prepare_singleshell at 103
   pnt = triangulate_seg(seg, cfg.spheremesh, ori);

>> ft_segment = prepare_localspheres(cfg,mri); gives me similar errors.

Any ideas how to troubleshoot these problems?

If it will help, (fiff_read_mri is a MNE-suite utility)

>> [stack] = fiff_read_mri('
Software/freesurfer/subjects/WS/mri/T1-neuromag/sets/COR.fif')

 	Creating tag directory for
/mnt/condor2/sameer/Software/freesurfer/subjects/WS/mri/T1-neuromag/sets/COR.fif...[done]
 	Reading slices..50..100..150..200..250..256..[done]

stack =

         id: [1x1 struct]
      trans: [1x1 struct]
     nslice: 256
     slices: [1x256 struct]

thanks for your time.

best,
sameer