It is actually in ?h.aparc.stats. The "total" is the total for the hemi
On 05/28/2015 09:12 AM, Hirsch, Gabriella wrote: > 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 > > -- 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
