oh, sorry, you'll need to recompute rvarmat (don't load rvar or beta)
[betamat rvarmat] = fast_glmfit(y,X);
Make sure you have $FREESURFER_HOME/fsfast/toolbox in your matlab path
doug
On 03/21/2013 05:04 PM, Laura M. Tully wrote:
> Hi Doug,
>
> I gave that a try but got a matrix error - below is the command line
> and error output from matlab, can you spot what I'm doing wrong? (I'm
> a matlab newbie I'm afraid...)
>
> y = load('contrast/cache.th13.abs.y.ocn.dat');
> X = load('Xg.dat');
> beta = inv(X'*X)*X'*y;
> C = load('contrast/C.dat');
> rvar = MRIread('rvar.mgh');
> betamat = fast_vol2mat(beta);
> rvarmat = fast_vol2mat(rvar);
> rhomat = fast_glm_pcc(betamat,X,C,rvarmat);
> rho = beta;
> rho.vol = fast_mat2vol(rhomat,rho.volsize);
> MRIwrite(rho,'contrast/pcc.mgh')
>
> ??? Error using ==> mtimes
> Inner matrix dimensions must agree.
>
> Error in ==> fast_glm_pcc at 39
> yhatd = Rd*(X*beta);
>
>
> Thanks!
>
> Laura
>
>
> On Thu, Mar 21, 2013 at 10:56 AM, Douglas N Greve
> <gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> It does it across the whole brain (on a voxel-by-voxel basis) but
> it is specific to the contrasts that you specify. You can run the
> same commands on the cluster averaged data (xxx.y.ocn...). To do
> this, don't load in the beta file. Instead
>
> y = load('xxx.y.ocn...');
> beta = inv(X'*X)*X'*y;
> then proceed with the rest of the code
>
> doug
>
>
>
> On 03/21/2013 01:49 PM, Laura M. Tully wrote:
>
> I had this exact question yesterday :-) The functions
> necessary to run it are in $FREESURFER_HOME/matlab and
> $FREESURFER_HOME/fsfast/toolbox
> Just add the path to these directories in your matlab (file ->
> setpath) and you can run the function from your matlab command
> window
>
> *Doug -* I had a follow up question about using this function
> on clusters identified in mri_glmfit-sim. Is the function as
> written below calculating the pcc across the whole brain or is
> it just calculating the rho using the betas specific to the
> cluster found in mri_glmfit-sim by only taking those betas
> from beta.mgh that are specific to the contrast and cluster
> results in C.dat? The reason I ask is that I have a cluster
> showing a significant relationship between thickness and a
> continuous behavioral variable (a positive relationship as
> denoted by a positive log10p of the Maxvertex in the cluster)
> and I'd like to get the correlation coefficient for it but
> when I run the PCC function I get zero so I'm wondering if
> this is because it is calculating across the whole brain
> rather than just within the cluster? (btw I get the same issue
> with a similar relationship showing positive corr between
> thickness and two behav variables).
> Thanks,
>
> Laura.
>
>
>
> On Thu, Mar 21, 2013 at 10:37 AM, Gabriel Gonzalez Escamilla
> <ggon...@upo.es <mailto:ggon...@upo.es> <mailto:ggon...@upo.es
> <mailto:ggon...@upo.es>>> wrote:
>
> Thanks Doug for your quick answer,
>
> Sorry for so late answer.
>
> One question about this, is about the fast_vol2mat, is this a
> function? if so, where can I get it?
>
> As the PCC is the R value, I'm guessing that I can just
> square at
> it, to obtain R2.
>
> When you asked me to divide the beta by sqrt(rvar), is
> there any
> place where I can find is this is the correct way to get the
> standardized beta?
>
> Best regards,
> Gabriel
>
>
>
> El 14/03/13, *Douglas Greve * <gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>
> <mailto:gr...@nmr.mgh.harvard.edu
> <mailto:gr...@nmr.mgh.harvard.edu>>> escribió:
>
>
> Hi Gabriel, I've attached a matlab routine which will
> compute the
> PCC. If you cd into the GLM dir, then
>
> X = load('Xg.dat');
> beta = MRIread('beta.mgh');
> C = load('yourcontrast/C.dat');
> rvar = MRIread('rvar.mgh');
>
> betamat = fast_vol2mat(beta);
> rvarmat = fast_vol2mat(rvar);
>
> rhomat = fast_glm_pcc(betamat,X,C,rvarmat);
>
> rho = beta;
> rho.vol = fast_mat2vol(rhomat,rho.volsize);
> MRIwrite(rho,'yourcontrast/pcc.mgh')
>
> The R2 should just be the square of the PCC, right?
>
> For the standardized beta, do you just divide the beta
> by sqrt(rvar)?
>
> doug
>
>
> On 3/14/13 1:39 PM, Gabriel Gonzalez Escamilla wrote:
>
>
> Dear Freesurfers
>
> I'm performing regression analyses including
> confounding
> variables, and I would like to know how to obtain
> the following
> information:
>
> A) The squre R
>
> and
>
> B) The standarized beta coefficient of an
> independient variable;
> and the partial correlation with its p-values
>
>
> Many thanks in advanced,
> Gabriel
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
> <Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> -- --------------------------
> PhD. student Gabriel González-Escamilla
> Laboratory of Functional Neuroscience
> Department of Physiology, Anatomy, and Cell Biology
> University Pablo de Olavide
> Ctra. de Utrera, Km.1
> 41013 - Seville
> - Spain -
>
> Email: ggon...@upo.es <mailto:ggon...@upo.es>
> <mailto:ggon...@upo.es <mailto:ggon...@upo.es>>
>
> http://www.upo.es/neuroaging/es/
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>
> <mailto:Freesurfer@nmr.mgh.harvard.edu
> <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> The information in this e-mail is intended only for the
> person to
> whom it is
> addressed. If you believe this e-mail was sent to you in
> error and
> the e-mail
> contains patient information, please contact the Partners
> Compliance HelpLine at
> http://www.partners.org/complianceline . If the e-mail was sent to
> you in error
> but does not contain patient information, please contact the
> sender and properly
> dispose of the e-mail.
>
>
>
>
> --
> --
> Laura M. Tully, MA
> Social Neuroscience & Psychopathology, Harvard University
> Center for the Assessment and Prevention of Prodromal States,
> UCLA Semel Institute of Neuroscience
> ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu>
> <mailto:ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu>>
> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu>
> <mailto:ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu>>
>
> 310-267-0170 <tel:310-267-0170>
> --
> My musings as a young clinical scientist:
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>
> Phone Number: 617-724-2358 <tel:617-724-2358>
> Fax: 617-726-7422 <tel:617-726-7422>
>
> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting>
> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
> Outgoing:
> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
>
>
>
>
> --
> --
> Laura M. Tully, MA
> Social Neuroscience & Psychopathology, Harvard University
> Center for the Assessment and Prevention of Prodromal States, UCLA
> Semel Institute of Neuroscience
> ltu...@mednet.ucla.edu <mailto:ltu...@mednet.ucla.edu>
> ltu...@fas.harvard.edu <mailto:ltu...@fas.harvard.edu>
> 310-267-0170
> --
> My musings as a young clinical scientist:
> http://theclinicalbrain.blogspot.com/
> Follow me on Twitter: @tully_laura
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
