still not sure, can you send these files? /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Avg-Intercept-thickness.mat /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contrasts/lh-Diff-EB-control-Intercept-thickness.mat
On 05/27/2015 04:30 PM, Hirsch, Gabriella wrote: > 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 > > > > _______________________________________________ > 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
