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/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 > > > > _______________________________________________ > 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
