Thank you so much Doug. We're mainly interested in controlling for Sex so it is great to know that it does work for DOSS.
Best, Fred > On Sep 5, 2017, at 18:07, Douglas N Greve <gr...@nmr.mgh.harvard.edu> wrote: > > For DOSS, It will work, but harder to set up the contrast matrices to > look at a sex effect. I would just do it coding males and females as > separate classes and not include sex as a variable > > >> On 09/05/2017 06:00 PM, Uquillas, Federico D'Oleire wrote: >> 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 >> >> > > -- > 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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