Dear John,
When I use the function to get brain volumes in ml that you kindly
provided I'm presented with this in matlab:
??? All rows in the bracketed expression must have the same
number of columns.
Error in ==>
/mrrc11/jupiter/SIMON_KELLER/OPTVBM_epilepsy/CONTROLS/7VOLUME/vol_calc.m
On line 10 ==> img = spm_slice_vol(V(i),spm_matrix([0 0
Any help would be appreciated.
With best wishes,
Simon
__________________________________________________________________
Simon Keller
The Magnetic Resonance and Image [log in to unmask]
Analysis Research Centre (MARIARC), Tel: 0151 794 5634
Pembroke Place, The University of Liverpool, Fax: 0151 794 5635
L69 3BX.
On Thu, 5 Sep 2002, John Ashburner wrote:
>> we are not sure if the file containing global mean intensity values to
>> enter as a covariate in the AnCova model is the "spm.ps". Can anybody help
>> us with this?
>
>The spm.ps file is PostScript containing various figures produced by SPM.
>I wouldn't suggest including this as a covariate.
>
>> Can you tell us which file contains the information about global mean
>> concentration (from smoothed unmodulated grey matter images) and global
>> mean volume values (from smoothed modulated grey matter images)?
>> We want to control for intensity and concentration/volume and don't
>> understand the best way to enter these covariates in the model.
>> Any suggestion will be very appreciated!
>
>The globals that SPM produces by default are not really ideal for using as
>regressors. The recent email sent to the list may help:
>
>> >> I am comparing patient and control groups on white and gray matter using
>> >> VBM method in SPM 99. Is it possible to use global gray or white matter
>> >> as a confounding covariate? If yes, how is it achieved?
>> >
>> >Just enter the values as covariates in the model. If you have the values
>> >stored as an ascii file, then you can enter spm_load instead, and SPM will
>> >prompt you for the ascii file. Alternatively, if you have the values
>> > stored in a variable in the Matlab workspace, then you can just enter the
>> > name of the variable.
>> >
>> >The following may be of interest (got them by searching for messages
>> >containing "VBM global" in the archives):
>> >
>> >http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0208&L=spm&P=R3815&I=-3
>> >http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0207&L=spm&P=R12913&I=-3
>> >http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0202&L=spm&P=R6740&I=-3
>> >http://www.jiscmail.ac.uk/cgi-bin/wa.exe?A2=ind0010&L=spm&P=R36678&I=-3
>
>More specifically, if you want tissue volumes in litres, then try:
>------------------------------------------------------------------
>function gl = get_integrals(P)
>% Integrate the values in an image.
>if nargin<1,
> P = spm_get(Inf,'*.img');
>end;
>V = spm_vol(P);
>gl = zeros(length(V),1);
>for i=1:length(gl),
> for z=1:V(i).dim(3),
> img = spm_slice_vol(V(i),spm_matrix([0 0 z]),V(i).dim(1:2),0);
> gl(i) = gl(i) + sum(img(:));
> fprintf('.');
> end;
> gl(i) = gl(i)*(det(V(i).mat)/100^3);
> fprintf('\n');
>end;
>------------------------------------------------------------------
>Note that if you are using spatially normalised images that have not been
>modulated, then the solution you get will not be the true tissue volume.
>Note also that the bottom of the brain is most probably chopped off the
>spatially normalised images, so you'll lose some of the cerebellar grey
>matter in the calculations.
>
>Best regards,
>-John
>--
>Dr John Ashburner.
>Functional Imaging Lab., 12 Queen Square, London WC1N 3BG, UK.
>tel: +44 (0)20 78337491 or +44 (0)20 78373611 x4381
>fax: +44 (0)20 78131420 http://www.fil.ion.ucl.ac.uk/~john
>
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