Sure thing, see attached. ________________________________________ 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: Wednesday, May 27, 2015 4:19 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size
Can you send me /media/seagate_external_/freesurfer_subjects/qdec/Untitled/qdec.fsgd On 05/27/2015 03:47 PM, Hirsch, Gabriella wrote: > Thanks for the response, Doug! > > Yes, here is the error message I get when I try to keep one measure (e.g. ICV > or global volume) in QDEC. As I said earlier, when I keep BOTH measures (like > keeping both ICV and global volume as nuisance factors) in a simple thickness > analysis between two groups, then the analysis is successful. If I only keep > one, then QDEC simply closes automatically and I get the attached error. I > kept everything qdec outputted for completeness in the attached .txt file. > > Interestingly, when I run mri_glmfit manually in the terminal, I can pose one > measure (e.g global volume) as a covariate without demeaning and the analysis > seemingly works (I don't get any errors, anyway). > > Thank you! > Gabriella > ________________________________________ > 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: Wednesday, May 27, 2015 3:23 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > > Hi Gabriella, sorry for the delay > > On 05/22/2015 09:15 AM, Hirsch, Gabriella 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 >> *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? >> > It may or may not be a problem depending on what you are doing. I prefer > to divide the glm input value by the ICV, but some like to use as a > regressor. If you want to do it that way, then you'll have to demean, or > you might try to just scale all ICVs to bring them into a range similar > to that of the input value. >> 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? >> > Saying that it crashes is not too informative. Can you give more info? > Eg, an error message? >> 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. >> > You can scale the input or scale the ICV as I mention above. You can > also run it as a DOSS (different offset, same slope) > doug >> I’d really appreciate any help on this. >> >> Thank you! >> >> Gabriella >> >> >> >> _______________________________________________ >> 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 > > > 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. > > > > > _______________________________________________ > 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
qdec.fsgd
Description: qdec.fsgd
_______________________________________________ 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.
