So this instead?
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);
[betamat rvarmat] = fast_glmfit(y,X);
rhomat = fast_glm_pcc(betamat,X,C,**rvarmat);
rho = beta;
rho.vol = fast_mat2vol(rhomat,rho.**volsize);
MRIwrite(rho,'contrast/pcc.**mgh')
On Thu, Mar 21, 2013 at 3:14 PM, Douglas N Greve
<gr...@nmr.mgh.harvard.edu>wrote:
> 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<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 <gr...@nmr.mgh.harvard.edu>>
>> <mailto:gr...@nmr.mgh.harvard.**edu<gr...@nmr.mgh.harvard.edu>
>>
>> <mailto:gr...@nmr.mgh.harvard.**edu <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
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>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>>
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>> >>
>>
>> <freesur...@nmr.mgh.harvard.**edu<Freesurfer@nmr.mgh.harvard.edu>
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>> >
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>>
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>> >>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**
>> freesurfer <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/<http://www.upo.es/neuroaging/es/>
>> ______________________________**_________________
>> Freesurfer mailing list
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>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>>
>>
>> <mailto:freesur...@nmr.mgh.**harvard.edu<Freesurfer@nmr.mgh.harvard.edu>
>> >>
>>
>>
>> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<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
>>
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>> If the e-mail was sent to
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>>
>> -- --
>> 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/<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<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>
>>
>> <http://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>
>>
>> <http://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/<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/ <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<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/ <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
ltu...@fas.harvard.edu
310-267-0170
--
My musings as a young clinical scientist:
http://theclinicalbrain.blogspot.com/
Follow me on Twitter: @tully_laura
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