Thank you Doug! One more question for clarification:
"You would remove the quadratic term from the FSGD file, then create an image of quadradic values for each veretx and pass that with --pvr to glmfit". My quadratic value (age-squared) is a constant per participant. Do you mean I should create an image file per subject, where each vertex has the same value, namely age-squared of that subject? Next I should concatenate these files in FSGD-order to create a stacked mgz file, right? Second question: is there a way to hierarchically order the pvr-s, such that pvr 1 can only be included when pvr 2 is also included? Thanks again, Lizanne From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve Sent: maandag 2 februari 2015 17:19 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] vertexwise statistical modeling On 2/2/15 3:56 AM, Schweren, LJS (med) wrote: Dear freesurfer experts, I investigate case-control differences in cortical thickness in a group of 11 to 30 year olds. I ran vertex-wise analyses with glmfit, with covariates age and age-squared, to take into account confounding by age as we have a very wide age range. I use monte-carlo simulation testing. What results is the following: - some clusters of between-group difference (which I was looking for, no worries here) - a cluster covering almost the entire cortex being negatively correlated to the linear age term (which I understand, overall decreasing CT with increasing age) - 2 small clusters correlated to the quadratic age term Given these results, if I want to model age optimally, I should include the quadratic age-term only in some vertices but not in others, right? I have two questions: 1. Is there a way to include different covariates in different vertices, still doing the vertex-wise analyses of the entire brain? You can use the per-vertex regressor option (--pvr) to mri_glmfit. So you would remove the quadratic term from the FSGD file, then create an image of quadradic values for each veretx and pass that with --pvr to glmfit. 2. I apply a cluster-size threshold for the initial results, because I want to be sure about the case-control clusters. However for the covariates, if I can optimize the model per vertex, I would rather not use this threshold to be more sensitive. How could I go about this? Uncorrected results are stored in the sig.mgh file doug Thank you, your help is very much appreciated! Best wishes, Lizanne ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ________________________________ De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.
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