Yes, it seems to be a qdec issue since mri_glmfit works by itself even without demeaning the larger values of ICV. Thanks anyway.
One unrelated questions since I have you here; does FS produce a "total" or "global" cortical surface area file along the lines of TotalGrayVol? I'm looking for the best measure to correct during a group surface area analysis. Thanks again for all your help. Gabriella -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Wednesday, May 27, 2015 5:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size Oh, sorry, this is not a problem with mri_glmfit as I had thought. It is a problem with qdec itself on your data. I'm not sure what to tell you because I can't debug it without your data (and maybe not even then). You can use mri_glmfit directly. doug On 05/27/2015 04:49 PM, Hirsch, Gabriella wrote: > Done. I wasn't sure if I had to put an email address for the recipient so I > put yours. Let me know if you figure it out! :) Thanks so much. > > Gabriella > > -----Original Message----- > From: freesurfer-boun...@nmr.mgh.harvard.edu > [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N > Greve > Sent: Wednesday, May 27, 2015 4:43 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > > Hmm, still can't replicate the error. Can you post this file to our > filedrop (see end of msg for url) > /media/seagate_external_/freesurfer_subjects/qdec/Untitled/y.mgh > > On 05/27/2015 04:40 PM, Hirsch, Gabriella wrote: >> Sure. >> ________________________________________ >> 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 4:35 PM >> To: freesurfer@nmr.mgh.harvard.edu >> Subject: Re: [Freesurfer] FW: correcting for brain size >> >> 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/ >> l h-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 >> >> >> >> _______________________________________________ >> 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
