Thanks David!
Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of David Vazquez Sent: Friday, May 22, 2015 6:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, I'm not an expert in freesurfer. I've worked with freesurfer for 5 years now. When we started I had the same problem when including ICV in the qdec table and running it as a nuisance variable. I'm assuming you have ICV in mm^3. Try converting it to cm^3 or dcm^3 in your qdec table. That worked for us. I think qdec might have a problem with numbers in the millions/hundred thousands. Just don't forget to reconvert when you are interpreting/writing your results or else it can get confusing. Maybe its just us, but when we use ICV as a covariate many, many significant clusters were diminished to nothing. Hope this helps. -David Vazquez PhD candidate in Cognitive Neuroscience University of California, Riverside NSF GRFP fellow On Fri, May 22, 2015 at 6:16 AM Hirsch, Gabriella <gabriella_hir...@meei.harvard.edu<mailto:gabriella_hir...@meei.harvard.edu>> wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. I’d really appreciate any help on this. Thank you! Gabriella _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu<mailto: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.
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