Dear Richard,
On Mon, 14 May 2012 18:16:32 -0700, Richard Binney <[log in to unmask]> wrote:
>Hi,
>
>Please please help me and explain.....
>
>I am running the longitudinal pipeline in VBM8 (just trying it on one
>subject). I have changed defaults in the cg_vbm8_defaults.m file (see
>below) to write various outputs but I don't think it's quite playing nice.
>
>It outputted...:
>
>pmean*_seg8.txt
>pmr*_seg8.txt (x2)
>wmrmean
>wp1mr (x2)
>wp2mr (x2)
>y_rmean (x1)
>
>y_ I assume is the deformation.I was expecting 2: 1 for timepoint 1 image
>and 1 for timepoint 2 image......why do I only have one?
>
Spatial normalization parameters are only obtained for the mean of all time points. See page 17 in the VBM8 manual for a scheme about the longitudinal processing pipeline:
http://dbm.neuro.uni-jena.de/vbm8/VBM8-Manual.pdf
>Where is my jacobian determinant image as requested? What would be the
>prefix for this?
In contrast to cross-sectional data where modulation is always necessary there is only subtle influence of modulation for longitudinal data because modulation is the same for all time points (see above). Thus, for longitudinal data we analyze rather absolute volume differences between the time points.
>
>See my config file below:
Most of these changes regarding the output file will not be used, while the changes of parameters will be considered.
Best,
Christian
__________________________________
Christian Gaser, Ph.D.
Departments of Psychiatry and Neurology
Friedrich-Schiller-University of Jena
Jahnstrasse 3, D-07743 Jena, Germany
Tel: ++49-3641-934752 Fax: ++49-3641-934755
e-mail: [log in to unmask]
http://dbm.neuro.uni-jena.de
>
>
>
>
>global vbm8
>
>% Estimation options
>%=======================================================================
>vbm8.opts.tpm = {fullfile(spm('dir'),'toolbox','Seg','TPM.nii')}; %
>TPM.nii
>vbm8.opts.ngaus = [2 2 2 3 4 2]; % Gaussians per class
>vbm8.opts.affreg = 'mni'; % Affine regularisation
>vbm8.opts.warpreg = 4; % Warping regularisation
>vbm8.opts.biasreg = 0.0001; % Bias regularisation
>vbm8.opts.biasfwhm = 60; % Bias FWHM
>vbm8.opts.samp = 3; % Sampling distance
>
>% Writing options
>%=======================================================================
>
>% segmentations:
>% native 0/1 (none/yes)
>% warped 0/1 (none/yes)
>% modulated 0/1/2 (none/affine+nonlinear/nonlinear only)
>% dartel 0/1/2 (none/rigid/affine)
>
>vbm8.output.bias.native = 1; %changed from 0 RJB
>vbm8.output.bias.warped = 1;
>vbm8.output.bias.affine = 0;
>
>vbm8.output.label.native = 1; % this is PVE label image; chaged to 1 RJB
>vbm8.output.label.warped = 1; %changed to 1 RJB
>vbm8.output.label.dartel = 0;
>
>% order is [native normalised modulated dartel]
>vbm8.output.GM.native = 0; % GM
>vbm8.output.GM.warped = 1; % GM changed from RJB
>vbm8.output.GM.mod = 2; % GM
>vbm8.output.GM.dartel = 2; % GM changed from 0 RJB
>
>vbm8.output.WM.native = 0; % WM
>vbm8.output.WM.warped = 1; % WM changed from 0 RJB
>vbm8.output.WM.mod = 2; % WM
>vbm8.output.WM.dartel = 0; % WM
>
>vbm8.output.CSF.native = 0; % CSF
>vbm8.output.CSF.warped = 0; % CSF
>vbm8.output.CSF.mod = 0; % CSF
>vbm8.output.CSF.dartel = 0; % CSF
>
>% jacobian determinant 0/1 (none/yes)
>vbm8.output.jacobian.warped = 1; %changed form 0 RJB
>
>% order is [forward inverse]
>vbm8.output.warps = [1 1]; % changed from 0 0 RJB
>
>% Extended writing options
>%=======================================================================
>vbm8.extopts.dartelwarp = 1; % dartel normalization: 0 - spm default; 1 -
>yes
>vbm8.extopts.darteltpm =
>{fullfile(spm('dir'),'toolbox','vbm8','Template_1_IXI550_MNI152.nii')}; %
>Indicate first Dartel template
>vbm8.extopts.print = 1; % Display and print results
>
>% bias correction options
>%=======================================================================
>vbm8.bias.nits_bias = 8;
>vbm8.bias.biasfwhm = 60;
>vbm8.bias.biasreg = 1e-6;
>vbm8.bias.lmreg = 1e-6;
>
>% realign options
>%=======================================================================
>vbm8.realign.halfway = 1; % use halfway registration: 0 - no; 1 - yes
>vbm8.realign.weight = 1; % weight registration with inverse std: 0 - no;
>1 - yes
>vbm8.realign.ignore_mat= 0; % ignore exisiting positional information: 0 -
>no; 1 - yes
>
>% apply deformations options
>%=======================================================================
>vbm8.defs.interp = 5; % 5th degree B-spline
>
>% expert options
>%=======================================================================
>vbm8.extopts.cleanup = 3; % Cleanup: 0 - no; 1 - light; 2 -thorough
>changed from 2 RJB
>vbm8.extopts.finalmask = 1; % Final masking: 0 - no; 1 - yes
>vbm8.extopts.gcut = 1; % Skull-stripping with graph-cut: 0 - no; 1
>- yes
>vbm8.extopts.kmeans = 1; % segmentation initialization: 0 - new
>segment; 1 - Kmeans
>vbm8.extopts.mrf = 0.15; % MRF weighting
>vbm8.extopts.sanlm = 2; % use SANLM filter: 0 - no SANLM; 1 - SANLM
>with single-threading; 2 - SANLM with multi-threading
>vbm8.extopts.bias_fwhm = 60; % FWHM of Kmeans internal bias correction
>
>% experimental (not yet working)
>%=======================================================================
>vbm8.extopts.mask =
>{fullfile(spm('dir'),'toolbox','vbm8','submask.nii')}; % mask for
>subcortical areas + ventricles
>vbm8.output.surf.dartel= 0; % WM-surface
>
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