Thanks Steve. BTW, you can use the --voxdump col row slice functionality with mri_glmfit to extract all that info from a single voxel (maybe a little easier than mri_segstats)
doug On 03/25/2014 06:10 PM, Hodge, Steven wrote: > Hi Lizanne, > > My method for determining the equivalent model in R is to extract > single-vertex data from y.mgh (used in the mri_glmfit model), import it into > R, and apply what I think is the same model. The expectation is that the > results from R should match that particular vertex's values in beta.mgh, > sig.mgh, F.mgh, etc. > > So my suggestion is to use mri_segstats to get data from one vertex and play > with it in SPSS to find the equivalent model. I'm guessing 'Direct (or > Standard)', but each stats package will have default methods for scaling > variables and coding factors that are only apparent when you compare results > between packages (mri_glmfit, SPSS, R, etc.) > > My virtual machine is down, otherwise I could test some this in SPSS ... > > Steve > . . . . . . . . . . . . . . . > Steven M. Hodge > Child and Adolescent Neurodevelopment Initiative S3-301 > University of Massachusetts Medical School > 55 Lake Avenue North > Worcester, MA 01655 > > steven.ho...@umassmed.edu > 774-455-4108 > ________________________________________ > From: Douglas N Greve [gr...@nmr.mgh.harvard.edu] > Sent: Tuesday, March 25, 2014 11:43 > To: freesurfer@nmr.mgh.harvard.edu; Hodge, Steven > Subject: Re: [Freesurfer] glmfit with correlated covariates > > Hi Lizanne, I do not use SPSS so I cannot comment on which model is > equivalent. BTW, if you can save the design an contrast matrices in text > form from SPSS, then you can feed them into mri_glmfit. I'm cc'ing > Steve Hodge who has been working on mapping R design matrices to FS on > the chance that he might have some insight. > doug > > On 03/25/2014 06:04 AM, L. Schweren wrote: >> // >> >> /Dear FreeSurfer experts, / >> >> // >> >> /Thank you for your fast reply. We are extracting cortical thickness >> values for statistical sub-analyses in SPSS (due to corrections >> required with regard to family relatedness within the data); therefore >> we want to be a 100% certain that the statistical model we use in SPSS >> is identical to the model used by mri_glmfit. Can you confirm that, >> out of the multiple linear regression types listed below, mri_glmfit >> makes use of the Direct (or Standard) regression model?/ >> >> // >> >> *Type* >> >> >> >> *Characteristics* >> >> Direct (or Standard) >> >> >> >> ·All IVs are entered simultaneously >> >> Hierarchical >> >> >> >> ·IVs are entered in steps, i.e., some before others >> >> ·Interpret: /R/^2 change, /F/ change >> >> Forward >> >> >> >> ·The software enters IVs one by one until there are no more >> significant IVs to be entered >> >> Backward >> >> >> >> ·The software removes IVs one to one until there are no more >> non-significant IVs to removed >> >> Stepwise >> >> >> >> ·A combination of Forward and Backward MLR >> >> // >> >> /Thank you again for your help, / >> >> // >> >> /Best wishes, / >> >> /Lizanne/ >> >> Date: Wed, 12 Mar 2014 11:04:00 -0400 >> >> From: Douglas Greve <gr...@nmr.mgh.harvard.edu> >> >> Subject: Re: [Freesurfer] glmfit with correlated covariates >> >> To: freesurfer@nmr.mgh.harvard.edu >> >> Message-ID: <53207760.8010...@nmr.mgh.harvard.edu> >> >> Content-Type: text/plain; charset="iso-8859-1" >> >> It is just a standard multiple regression analysis where all regressors >> >> are fit simultaneously. One weight does not include that of another >> weight. >> >> doug >> >> On 3/12/14 5:16 AM, L. Schweren wrote: >> >>> Dear FreeSurfer experts, >>> I am attempting to disentangle the effects of different features of >>> pharmacological treatment on cortical thickness. >>> I am running glmfit from the commandline, with multiple covariates >>> (a.o. Z_Age, Z_TreatmentDuration and Z_StartAge) in the fsgd-file. >>> These covariates are correlated up to approximately 0.6 , which to my >>> understanding is not ideal yet not inducing collinearity. Running >>> glmfit, I do not get any errors such as ill-designed matrix or so. >>> My question regards the way the different regression weights are >>> calculated in each voxel. If I test the variance in CT of voxel A >>> explained by for example TreatmentDuration, and part of the variance >>> in voxel A is explained by both TreatmentDuration and StartAge, will >>> the regression weigth of TreatmentDuration than include the part that >>> is also explained by StartAge? Or are all other covariates first >>> "regressed out" of the variance, such that the variable I test can >>> only explain the variance that was not explained by any of the other >>> covariates? >>> Thank you very much, your help is very much appreciated! >>> Best wishes, >>> Lizanne >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> _______________________________________________ >> 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/ > > > > 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. > > > _______________________________________________ > 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
