On Thu, 28 Jul 2005 15:13:48 +0200, Diana Tordesillas
<[log in to unmask]> wrote:
>Hi Marko,
>
>First of all, thanks a lot for the information. I'm using SPM2 and I
don't find "spm_sn3d" on it, could you tell me where I can fin it?
>
>Thank you!!
>
>Best regards,
>
>Diana
For SPM2, it appears the file you want is spm_normalise.m. Parameter is
flags.smosrc.
function params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% Spatial (stereotactic) normalization
%
% FORMAT params = spm_normalise(VG,VF,matname,VWG,VWF,flags)
% VG - template handle(s)
% VF - handle of image to estimate params from
% matname - name of file to store deformation definitions
% VWG - template weighting image
% VWF - source weighting image
% flags - flags. If any field is not passed, then defaults are
assumed.
% smosrc - smoothing of source image (FWHM of Gaussian in mm).
% Defaults to 8.
% smoref - smoothing of template image (defaults to 0).
% regtype - regularisation type for affine registration
% See spm_affreg.m (default = 'mni').
% cutoff - Cutoff of the DCT bases. Lower values mean more
% basis functions are used (default = 30mm).
% nits - number of nonlinear iterations (default=16).
% reg - amount of regularisation (default=0.1)
%
___________________________________________________________________________
>
>Marko Wilke <[log in to unmask]> escribió:
>Hi Diana,
>
>> 1. I'm trying to reduce the amount of smoothing used in the
>> normalisation protocol. Is any way to do it? Which is the minimum
>> allowed by the program?
>
>There are certainly more elegant ways but if you call spm_sn3d, you can
>specify the smoothign via the command line. Check the file for
>instructions, as in
>
>% FORMAT spm_sn3d(P,matname,bb,Vox,params,spms,brainmask, objmask)
>% P - image(s) to normalize
>% matname - name of file to store deformation definitions
>% bb - bounding box for normalized image
>% Vox - voxel sizes for normalized image
>% params(1) - number of basis functions in X
>% params(2) - " " " " " Y
>% params(3) - " " " " " Z
>% params(4) - number of iterations for elastic deformation
>% Setting any of these parameters to 0 will force
>% the program to perform only the affine
>% normalization.
>% params(5) - smoothing for image (mm).
>% params(6) - amount of regularization. Higher values produce smoother
>deformation
>% fields.
>
>Parameter 5 is what you're looking for. Make sure your template is
>smoothed by the same kernel you specify here.
>
>Best,
>Marko
>--
>=====================================================================
>Marko Wilke (Dr.med./M.D.)
>[log in to unmask]
>
>Universitäts-Kinderklinik University Children's Hospital
>Abt. III (Neuropädiatrie) Dept. III (Pediatric neurology)
>Hoppe-Seyler-Str. 1, D - 72076 Tübingen
>Tel.: (+49) 07071 29-83416 Fax: (+49) 07071 29-5473
>=====================================================================
>
>
>---------------------------------
>
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