MNI aligned grids, mris and segmentation

Sameer Walawalkar sameer at ANDREW.CMU.EDU
Tue Mar 20 19:10:36 CET 2007

Dear Robert,

Thank you for your reply to my question about (MNI aligned grids, MRIs and
segmentation).  I am going to take your advise of exploring single subject
beamed data. But, I want to clarify one or two points before going on.

I am using Neuromag 306 data. Or the MRIs, I have already used MNE to
generate bem head model meshes stored in files of kind
<something>_bem_sol.fif, but which fieldtrip program do I use to extract
this (the info is for ctf and I could not find an intuitive or obvious
extension to my case).

Can I simply proceed as

bem_head = appropriate-field-trip-function(<something>_bem_sol.fif);
hdr = read_fcdc_header(datafile.fif);

cfg = [];
cfg.grad = hdr.grad;
cfg.vol = bem_head;
cfg.resolution = 1;
grid_bem = prepare_leadfield(cfg);

Also am not sure how to extract head shape which is needed for plotting
headmodel. Is it shimply the HPI coils information ?

thanks for your time.


On Mon, 19 Mar 2007, Robert Oostenveld wrote:

> Hi Sameer
> On 13 Mar 2007, at 15:27, Sameer Walawalkar wrote:
>> 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)
>> From (
>> id=fieldtrip:documentation:create_single-
>> subject_grids_in_individual_head_space_that_are_all_aligned_in_mni_space)
> I suggest that you also look at
> doku.php?
> id=fieldtrip:documentation:make_leadfields_using_different_headmodels
>> Here, in the very beginning,
>> ...
>> 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.
> The idea here is to use an existing template MRI to construct a headmodel,
> and define a dipole grid in it. Then, each individual MRI is warped to the
> template MRI, and the inverse of that warp is applied to the dipole grid.
> Subsequently, an individual headmodel is made for each individual MRI and the
> warped dipole grid (in individual subjects' coordinates) is used together
> with the individual headmodel for the beaming. The source reconstructions are
> computed, and can immediately be averaged over subjects. The underlying
> motivation relates to group statistics without the neccessity to interpolate
> the source reconstructions to an artifical higher resolution.
> Since you are just starting with beamforming, I advice that you do not
> immediately try to follow the "MNI common grids" approach. Better is first to
> explore some single subject beamed data.
>> Can I give the path to my dicom mri images directory and the name of a file
>> ending in .dcm?
>> Incidently
>>>> mri =
>> read_fcdc_mri('Z:\KarmaCond\BIRC_images_foolaround\070207134421\2
>> \02-0001-000001.dcm');
>> ??? Undefined function or variable "hdr".
>> Error in ==> read_fcdc_mri at 179
>>   [z, indx]   = sort(cell2mat({hdr.SliceLocation}));
> If you have the image processing toolbox, you should be able to read in a set
> of DICOM files. Note that the homogenous transformation matrix then is not
> yet correct, i.e. the slice resolution and spacing and the coordinate axes
> are not yet specified. Figuring the slice ordering from a set of loose dicom
> files is tricky. I think that the naming of your dicom files differs from
> ours, we have a directory containing files like this:
> 2.92.2003.
> 2.93.2003.
> 2.94.2003.
> 2.95.2003.
> 2.96.2003.
> 2.97.2003.
> 2.98.2003.
> 2.99.2003.
> The detection of the correct dcm files in your directory seems not to work. I
> suggest that you set a debugger breakpoint in read_fcdc_mri and that you step
> through it one line at a time.
> best regards,
> Robert

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