Thanks everyone - just what I needed to know. So I should add a cell array called 'orth' to my "multiple conditons" onsets file that already contains names, onsets, durations and pmod? Am I right in thinking that this will turn off orthogonalisation for any parametric modulators attached to each condition?
B.
-----Original Message-----
From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of Guillaume Flandin
Sent: 07 October 2016 19:17
To: [log in to unmask]
Subject: Re: [SPM] orthogonalisation parametric modulators spm12
Hi Steve & Becky,
you can also switch on or off orthogonalisation when using the "multiple conditions" option by providing a cell array named 'orth' containing true/false for each condition.
It was not mentioned in the help text until recently (but will be in the (soon to come) public update).
Best regards,
Guillaume.
On 07/10/16 19:02, Steve Fleming wrote:
> Hi Becky,
>
> As Cyril says in the GUI you can switch it on or off when you specify
> conditions, but it's on by default.
>
> For scripting you can pass it in as a flag in the matllabbatch
> structure, e.g.:
>
> matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).name = 'ConditionName'
> matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).onset =
> yourOnsetVector matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).pmod(1).name = 'PmodName'
> matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).pmod(1).param =
> yourPmodVector
> matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).pmod(1).poly = 1
>
> matlabbatch{1}.spm.stats.fmri_spec.sess(1).cond(1).orth = 0 or 1
>
> So this way you can set orthogonalisation on and off flexibly within
> each condition (onset).
>
> However if you're passing in names, onsets and durations cell arrays
> as part of a "multiple conditions" .mat file I don't know whether
> there's a way to set this globally (and if you don't it will remain
> on). For this reason we've switched to the above method in our scripts.
>
> Hope that helps
>
> cheers
> Steve
>
> On 6 October 2016 at 19:26, PERNET Cyril <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> in the latest version this is optional ...
>
>
> --
> Dr Cyril Pernet,
> Senior Academic Fellow, Neuroimaging Sciences
> Centre for Clinical Brain Sciences (CCBS)
>
> The University of Edinburgh
> Chancellor's Building, Room GU426D
> 49 Little France Crescent
> Edinburgh EH16 4SB
> [log in to unmask] <mailto:[log in to unmask]>
> <http://www.sbirc.ed.ac.uk/cyril>http://www.sbirc.ed.ac.uk/cyril
> <http://www.sbirc.ed.ac.uk/cyril>
> http://www.ed.ac.uk/edinburgh-imaging
> <http://www.ed.ac.uk/edinburgh-imaging>
>
> ------------------------------------------------------------------------
> *From:* SPM (Statistical Parametric Mapping) <[log in to unmask]
> <mailto:[log in to unmask]>> on behalf of Lawson, Rebecca
> <[log in to unmask] <mailto:[log in to unmask]>>
> *Sent:* 06 October 2016 18:48:06
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> *Subject:* [SPM] orthogonalisation parametric modulators spm12
>
>
> Hello,____
>
> __ __
>
> Quick Question. Is orthogonalisation of parametric modulators still
> hard coded in SPM12 (as in previous versions e.g.
> http://imaging.mrc-cbu.cam.ac.uk/imaging/ParametricModulations
> <http://imaging.mrc-cbu.cam.ac.uk/imaging/ParametricModulations>)
> and, if so, which lines of code in which functions need to be
> commented out to turn it off? I can guess (based on the CBU
> instructions pertaining to SPM8) but I just wanted to check for
> definite. ____
>
> __ __
>
> Thanks,____
>
> B.____
>
>
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>
> --
> Stephen M. Fleming PhD
> Principal Research Associate
> Wellcome Trust Centre for Neuroimaging, UCL
> +44 (0)20 344 84349 | metacoglab.org <http://metacoglab.org> |
> +@smfleming
>
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG
|