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Dear Priya,
just to add that if Y contains a mean fMRI time series and X is a matrix
of confounds then you can compute:
% residual forming matrix:
R = eye(size(X,1)) - X*pinv(X);
% residuals:
r = R * Y;
A related function in SPM would be spm_ancova.m.
Best regards,
Guillaume.
On 08/01/16 03:48, Priya Aggarwal wrote:
> Thank you so much! this code is very useful...:)
>
> On Thu, Jan 7, 2016 at 9:40 PM, <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> The stats toolbox has a regress function. The neural network toolbox
> has a function regression, which I think is not as good as you would
> need to extract residuals on your own. ____
>
> __ __
>
> I attached a function I wrote for this, which also removed a 3^rd
> order poly from the data. It needs CSF and WM masks in nii files,
> and was really specifically written for one data set of mine, but
> you are free to steal any code if it is helpful. I certainly won’t
> work out of the box on anything though, it was a one-study-use
> function. : )____
>
> __ __
>
> __ __
>
> Colin Hawco, PhD____
>
> Neuranalysis Consulting____
>
> Neuroimaging analysis and consultation____
>
> www.neuranalysis.com <http://www.neuranalysis.com>____
>
> [log in to unmask] <mailto:[log in to unmask]>____
>
> __ __
>
> __ __
>
> __ __
>
> *From:*SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask] <mailto:[log in to unmask]>] *On Behalf
> Of *Priya Aggarwal
> *Sent:* January-07-16 12:59 AM
> *To:* [log in to unmask] <mailto:[log in to unmask]>
> *Subject:* Re: [SPM] linear regression of cofounds____
>
> __ __
>
> Thank you for this information!____
>
> __ __
>
> I would like to use matlab for removing cofounds. Is there any
> inbuild command for running regression in matlab.____
>
> __ __
>
> Thanks,____
>
> Priya____
>
> __ __
>
> On Thu, Jan 7, 2016 at 12:41 AM, <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:____
>
> You have a few options. You can download an existing Matlab toolbox,
> such as the Conn toolbox, which has some of this functionality built in.
>
> Personally I tend to code these things myself. You can grab the
> nifti toolbox for Matlab (off NITRICS), which will allow you to load
> your images as Matlab variables (I find it a bit easier to use than
> SPM's functions).
>
> Then loop through voxels, run regress in matlab on the time series,
> and save the residuals into a new data structure.
>
> If you want to do a really good job removing motion effects, I would
> suggest using the Pythagorean transform of the motion parameters
> (Damion Faire did some good work on this), of if you are more
> ambitious use a voxel-specific set of regressors as done by Ted
> Satterthwaite
>
> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3811142/
>
> Which really seems to make a difference in removing motion effects,
> especially for analysis between groups where motion may differ, a
> major confound in most analyses.
>
> Good luck!
>
> Colin Hawco, PhD
> Neuranalysis Consulting
> Neuroimaging analysis and consultation
> www.neuranalysis.com <http://www.neuranalysis.com>
> [log in to unmask] <mailto:[log in to unmask]>____
>
>
>
>
> -----Original Message-----
> From: SPM (Statistical Parametric Mapping)
> [mailto:[log in to unmask] <mailto:[log in to unmask]>] On Behalf Of
> Priya Aggarwal
> Sent: January-06-16 12:18 PM
> To: [log in to unmask] <mailto:[log in to unmask]>
> Subject: [SPM] linear regression of cofounds
>
> Hi everyone,
>
> I want to regress out various cofounds (such as realignment
> parameters and its derivative, white matter signal etc.) from my
> regional mean fMRI time series. This linear regression is essential
> step in resting state fMRI functional connectivity analysis.
>
> Can anyone please help me how can i do it?
>
> Thank you for this help!
>
> regards,
> Priya____
>
>
>
> ____
>
> __ __
>
> -- ____
>
> Thanks and Warm Regards,____
>
> __ __
>
> Priya Aggarwal____
>
> Indraprastha Institute of Information Technology, Delhi (IIIT-D)____
>
> Okhla Industrial Estate,Phase III
> (Near Govind Puri Metro Station)
> New Delhi, India - 110020____
>
>
>
>
> --
> Thanks and Warm Regards,
>
> Priya Aggarwal
> Indraprastha Institute of Information Technology, Delhi (IIIT-D)
> Okhla Industrial Estate,Phase III
> (Near Govind Puri Metro Station)
> New Delhi, India - 110020
--
Guillaume Flandin, PhD
Wellcome Trust Centre for Neuroimaging
University College London
12 Queen Square
London WC1N 3BG