That's what I thought but it doesn't seem to be there; I only have the following:
BrainSegVol BrainSegVolNotVent BrainSegVolNotVentSurf lhCortexVol rhCortexVol CortexVol lhCorticalWhiteMatterVol rhCorticalWhiteMatterVol CorticalWhiteMatterVol SubCortGrayVol TotalGrayVol SupraTentorialVol SupraTentorialVolNotVent SupraTentorialVolNotVentVox MaskVol BrainSegVol-to-eTIV MaskVol-to-eTIV lhSurfaceHoles rhSurfaceHoles SurfaceHoles eTIV Is there a way to create it? Thanks! ________________________________________ 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 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size There should be one in aseg.stats. On 05/27/2015 05:45 PM, Hirsch, Gabriella wrote: > 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 > > -- 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
