Appreciate the quick reply. I may be re-framing my question a bit here, but I'm curious as to the context in which one would use the PCA analysis. Is it meant primarily for functional data or can it be applied to glmfits for structural data? When I ran this the first time, I got 14 eigenvalues on a subset of 14 participant MPRAGE's from a large dataset to test the --pca flag (I haven't seen much about it on the documentation). In hindsight, I think the 14 eigenvalues I'm getting are actually the number of participants in the study, which means I am probably using this flag in the wrong context. I'm curious about using this on a larger dataset from different types of scanners and finding components unique to scanner type using pca that can be addressed in later group analyses. Given that PCA uses "temporal" components (if you don't mind could you expand on this?) can it even be applied to morphological data like individual T1 images? Or should it be used solely in isolation with functional images for individual subjects (such as the way GIFT or ICA toolboxes would?).
Basically I'd like to know conceptually when you would use this and what it is capable of doing. My apologies if that is a horrible combination of vague and broad. On Thu, Dec 4, 2014 at 1:50 PM, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > It performs pca/svd on the residuals. The sdiag.mat I think includes the > singular values but also the percent variance explained by each > component and the cumulative explained by all components upto and > including that component. You probably just need to change the overlay > thresholds on the v.mgh to make it look more reasonable. The range of > the singular values depends on your data so you can't just look at them > and decide they are too big. The u.mtx are the "temporal" components. > > doug > > On 12/04/2014 11:10 AM, Thomas DeRamus wrote: > > Dear Freesurfer experts, > > > > Potentially super-noob question here, but I'm curious about the --pca > > flag on mri_glmfit. I can see that it does PCA/SVD on the dataset? in > > question and saves the residuals to the glmdir specified, but I was > > unable to find anything in the documentation describing what exactly > > it is doing. I got sdiag.mat, stats.dat (with some rather large > > eigenvalues, on the order of 40k, but they might look more normal once > > I demean my variables), a u.mtx, a v.mgh surface overlay, and an error > > log (stating MatlabRead: readHeder returned NULL, ImageRead > > (/path/glmdir/pca-eres/sdiag.mat) failed. When I loaded the v.mgh, it > > looked rather binarized (with red and blue colors covering the entire > > cortex mask for that hemi). > > > > May I ask how it is computing these eigenvalues? What the sdiag and > > u.mtx files are used for? And what is being displayed in the v.mgh (is > > it components? if so, what do these components reflect?). And most > > importantly, is this meant primarily for functional data or can it be > > applied to mophometric data? If it can be used for the latter, what is > > being fed into the PCA/SVD to determine spatial components? > > > > -- > > *Thomas DeRamus* > > UAB Department of Psychology, Behavioral Neuroscience > > Graduate Research Trainee > > Civitan International Research Center > > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 > > _Phone_: 205-934-0971 _Email:_ tpdera...@gmail.com > > <mailto:tpdera...@gmail.com>, faus...@uab.edu <mailto:faus...@uab.edu> > > > > > > _______________________________________________ > > Freesurfer mailing list > > Freesurfer@nmr.mgh.harvard.edu > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > 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: https://gate.nmr.mgh.harvard.edu/filedrop2 > 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 > > > 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. > > -- *Thomas DeRamus* UAB Department of Psychology, Behavioral Neuroscience Graduate Research Trainee Civitan International Research Center 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 *Phone*: 205-934-0971 *Email:* tpdera...@gmail.com, faus...@uab.edu
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