External Email - Use Caution Perfect! Thanks so much. ________________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <dgr...@mgh.harvard.edu> Sent: 08 October 2019 21:30 To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area
You can add --jac to to the mri_surf2surf command to get jacobian correction. If you use mris_preproc with --meas area (or volume), it will automatically do it On 10/8/19 3:07 PM, Linn Christin Bonaventure Norbom wrote: > > External Email - Use Caution > > Thanks so much for the reply. > > I am performing linked-ICA on cortical thickness, grey-/white matter > contrast (GWC), and cortical surface area, and I must admit I sampled > the surfaces onto fsaverage in an identical way across modalities > using surf2surf. I have attached the code for fsaverage re-sampling of > area. > > While I found a global signal for GWC and thickness in my analyses, I > found no global signal for surface area (and also no main effect of > sex which was unexpected). > > So if I understand correctly: > -my results are probably off as I have not performed the Jacobian > correction that retains the information of global surface area when > mapping onto fsaverage using surf2surf? > -Is there a "Jacobian flag" that can be added to the surf2surf code? > If else it appeared that the correction is default if > running mri_preproc on area, is that correct? > > Thanks so much for helping me out with this, I really appreciate it! > Linn > > > ------------------------------------------------------------------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas > N.,Ph.D. <dgr...@mgh.harvard.edu> > *Sent:* 07 October 2019 16:50 > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Main effect of sex for total surface area, > but not for summed vertex-wise surface area > How did you map the area to fsaverage? If you don't do it properly, > you can get some funny results because area has to be jacobian corrected. > > On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote: >> >> External Email - Use Caution >> >> Hello all Freesurfer experts! >> >> Through my analysis I found that, if I plot the "white surface >> total area" found in subjid/stats/?h.aparc.stats by sex, I as >> expected find that males have overall larger surface area as compared >> to females. >> >> When plotting the summed verticies of ?h.area for each person on the >> other hand (albeit after mapping the ?h.area to fsaverage), this main >> association with sex is not at all present. I am a bit puzzled by >> this and I am wondering if some sort of global scaling is performed >> when computing vertex-wise surface area? So that corresponding >> differences in vertex-wise area are relative sex differences? >> >> I understand that area at a single vertex does not hold biological >> relevance in the same way that for instance thickness does, but >> unfortunately I still don't quite understand the differing sex >> associations between aparcs total surface area and the summed >> vertex-wise surface area. >> >> Thanks so much in advance! >> Kind regards Linn >> >> >> _______________________________________________ >> 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 _______________________________________________ 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
