I was actually looking for total area.pial surface..? Sorry, I forget FS calls it area.pial while area is wm. Is there a way to find this value?
Gabriella -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas N Greve Sent: Thursday, May 28, 2015 2:20 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: correcting for brain size isn't that what you are looking for? On 05/28/2015 02:05 PM, Hirsch, Gabriella wrote: > Hmm, I tried looking and all I can find is total wm surface area and surface > area of individual regions. I've attached an lh.aparc.stats file for one of > the subjects. Am I missing something? > > Thanks so much! > > > ________________________________________ > 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: Thursday, May 28, 2015 1:37 PM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] FW: correcting for brain size > > 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/contras >>>>> ts/ >>>>> lh-Avg-Intercept-thickness.mat >>>>> >>>>> /media/seagate_external_/freesurfer_subjects/qdec/Untitled/contras >>>>> ts/ 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.f >>>>>> sgd >>>>>> >>>>>> 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 > > > > _______________________________________________ > 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
