MNI aligned grids, mris and segmentation

Sameer Walawalkar sameer at ANDREW.CMU.EDU
Tue Mar 13 15:27:56 CET 2007


I want to start DICS analysis of my MEG data. For this I need to have MRI
and MEG data coregistered. I also need multisphere forward models for
which segmentation is necessary.

Am I correct in understanding that the following webpage contains info
about segmentation? (in addition to MNI aligning all grids)


Here, in the very beginning,

SUBJ         = {'subj1','subj2','subj3'};
PREINMRI     = '~/mri/';
PREOUT       = '~/grids/';
TEMPL        = 'mni_standards/t1_icbm_normal_1mm_pn0_rf0.mnc';
RES          = 1;   % grid resolution [cm]
OUTWARDSHIFT = 1.5; % outwardshift for inside/outside detection [cm]

% segment the template brain and construct volume
templmri = read_fcdc_mri(sprintf('%s%s',PREINMRI,TEMPL));
clear cfg;
cfg.coordinates = 'spm';
seg = volumesegment(cfg,templmri);
vol = prepare_singleshell([],seg);

I understand that in the commands above, first we are creating a template
mri to which all other grids will later be aligned. What exactly is
t1_icbm_normal_1mm_pn0_rf0.mnc  ? Is it a slice from an mri image.
Can I give the path to my dicom mri images directory and the name of a
file ending in .dcm?

>> mri =
??? Undefined function or variable "hdr".

Error in ==> read_fcdc_mri at 179
   [z, indx]   = sort(cell2mat({hdr.SliceLocation}));

Thanks you very much.


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