Thank you Doug. Is the one that doesn't fail okay? Best,
Fred > On Sep 5, 2017, at 16:57, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > in the one that fails you are including the binary gender as a > continuous variable, which will fail in FSGD. All catagorical variables > need to be coded as classes. see > https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples > > >> On 09/05/2017 03:07 PM, Uquillas, Federico D'Oleire wrote: >> Dear Doug, >> >> Sending the FSGD described in our original email as failing due to it being >> "ill-conditioned or badly scaled" with DOSS [0 1 0 0 0]. It is titled >> "FAILS_N47_edited_BL_CT_PiB_centAge_fsgd.txt". >> >> The other one is the one that runs and gives expected results with a DOSS >> contrast [0 1 0 0]. >> >> Thanks so much. >> >> Best regards, >> >> Fred >> >> ________________________________________ >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve >> [gr...@nmr.mgh.harvard.edu] >> Sent: Tuesday, September 05, 2017 12:01 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] controlling for Sex in a model using two >> continuous variables onto CTh >> >> can you send the fsgd file for the analysis that is failing? >> >> >>> On 08/29/2017 02:29 PM, Uquillas, Federico D'Oleire wrote: >>> Dear FreeSurfer experts, >>> >>> We have run a vertex-wise analysis regressing a continuous variable >>> onto cortical thickness on the surface, and would like to verify that >>> our contrast that uses Age and Sex as covariates was defined >>> correctly, especially since there is probably more than one way to >>> control for a binary variable like Sex. >>> >>> On the website (https://surfer.nmr.mgh.harvard.edu/fswiki/DodsDoss) it >>> suggests to make two regressors, one for Males, and one for Females, >>> where for the former a 1 is indicative of the Male category, and a 1 >>> on the latter is indicative of the Female category. However, using >>> that FSGD file and running a DOSS contrast as [0 1 0 0 0], we get the >>> error: matrix is ill-condition or badly scaled, condno=2.01889e+07. >>> We believe this may be due to the fact that Male and Female categories >>> are autocorrelated and Freesurfer likes variables to be de-meaned. >>> Running a FSGD file with only Age and our variable of interest via a >>> DOSS contrast of [0 1 0] works without any errors. >>> >>> We thus created an FSGD file where we have Sex as our third variable >>> (in addition to our continuous variable of interest and one demeaned >>> continuous covariate), coding 1s for Males and 0s for Females, and we >>> used a DOSS contrast of [0 1 0 0]. This provided us with a map that >>> makes sense with our expectations. >>> >>> We would like to verify if this is doing what we believe it is doing; >>> that is, looking at the relationship of our continuous variable or >>> interest after accounting for age and sex. >>> Any thoughts would be greatly appreciated. >>> >>> Thank you so much. >>> >>> Best, >>> >>> Fred >>> >>> >>> >>> >>> >>> _______________________________________________ >>> 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 >> >> >> _______________________________________________ >> 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 _______________________________________________ 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 . 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