[Freesurfer] Covary for a categorical variable in mri_glmfit
Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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.
Re: [Freesurfer] Covary for a categorical variable in mri_glmfit
I still don't know what you mean by covarying for gender. What is your design? Can you send your FSGD file? doug On 09/05/2012 04:44 PM, Jeff Sadino wrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html ___ 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.
Re: [Freesurfer] Covary for a categorical variable in mri_glmfit
Hello, I think our emails were getting crossed in cyberspace. I have a group that has a disproportionate number of females, and so there is a significant difference in the number of females as compared to males (chi-square p=.01). This must be accounted for. If I find that one group has a smaller brain volume, etc., then it could be attributed to one group having fewer females than the others. My ultimate goal is to run an analysis on the thickness, taking into account these sex differences (and ICV and age). My plan was to covary for sex, icv, and age. I have covaried for icv and age lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino jsadino.que...@gmail.comwrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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.
Re: [Freesurfer] Covary for a categorical variable in mri_glmfit
Use gender as a discrete variable in the FSGD, ie, a class for M and a class for F. If you have two other groups (say, normals and patients), then use four classes (Mnormals, Mpatients, etc). Then test for the normals vs patients with (Mnorm+Fnorm) - (Mpat+Fpat). This regresses out gender. doug On 9/5/12 8:10 PM, Jeff Sadino wrote: Hello, I think our emails were getting crossed in cyberspace. I have a group that has a disproportionate number of females, and so there is a significant difference in the number of females as compared to males (chi-square p=.01). This must be accounted for. If I find that one group has a smaller brain volume, etc., then it could be attributed to one group having fewer females than the others. My ultimate goal is to run an analysis on the thickness, taking into account these sex differences (and ICV and age). My plan was to covary for sex, icv, and age. I have covaried for icv and age lots of times, but I am having trouble covarying (if that is the right word) for this categorical sex variable. Any help would be greatly appreciated! Jeff On Wed, Sep 5, 2012 at 10:44 AM, Jeff Sadino jsadino.que...@gmail.com mailto:jsadino.que...@gmail.com wrote: Hello, I am trying to covary for Gender in mri_glmfit, but I am having errors pop up. I tried to follow Doug's suggesting in this post: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg12272.html but after modifying my Xg.dat file and rerunning mri_glmfit, it says: ERROR: matrix is ill-conditioned or badly scaled, condno = 1.53319e+07 I can run it using the --illcond flag, but then I get a bunch of: *** CEPHES ERROR: fdtrc domain error *** Can anyone please give advice on how to covary for Gender in mri_glmfit (or qdec)? As always, thank you for all of your great help!! Jeff Sadino ___ 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 . 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.
