The flag to preserve area is not being turned on there. You can try running mris_preproc separately for area and including the --jac flag. If that does not work, you can download version6 and just use it to run mris_preproc
On 8/10/18 4:41 PM, Derek Sayre Andrews wrote:
External Email - Use Caution
Hi Douglas,
Of course, please find attached a copy of the recon-all.log file.
Best, Derek
PS: Apologies for the direct email in order to get you the attachment
cid:image001.png@01D430A0.A5153C80
*Derek Sayre Andrews, PhD*
Postdoctoral Scholar
Department of Psychiatry and Behavioral Sciences
The M.I.N.D Institute
University of California Davis
Telephone: +1 916 703 0360 Email: dandrews@UCDavis.edu mailto:dandrews@UCDavis.edu
*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edu *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Friday, August 10, 2018 at 11:12 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children
Yes. -qcache actually calls mris_preproc. At one point, FS did not preserve total area when mapping to fsaverage. I fixed it a while ago, but maybe something was still off in 5.1
On 8/10/18 2:06 PM, Derek Sayre Andrews wrote:
* External Email - Use Caution * Hi Douglas, Thank you for the response. I did not use mris_preproc to prepared the data. The data was mapped to fsaverage using recon-all with -qcache. I then loaded the l/rh.area.pial.fwhm15.fsaverage.mgh files into MATLAB using SurfStatReadData <http://www.math.mcgill.ca/keith/surfstat/> and summed them across each vertex. Would the terminal output of recon-all -qcache be helpful? Best, Derek cid:part2.2B5BCEFF.1D6DDEE5@mgh.harvard.edu *Derek Sayre Andrews, PhD* Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews@UCDavis.edu <mailto:dandrews@UCDavis.edu> *From: *<freesurfer-bounces@nmr.mgh.harvard.edu> <mailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Douglas Greve <dgreve@mgh.harvard.edu> <mailto:dgreve@mgh.harvard.edu> *Reply-To: *Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Date: *Friday, August 10, 2018 at 10:25 AM *To: *"freesurfer@nmr.mgh.harvard.edu" <mailto:freesurfer@nmr.mgh.harvard.edu> <freesurfer@nmr.mgh.harvard.edu> <mailto:freesurfer@nmr.mgh.harvard.edu> *Subject: *Re: [Freesurfer] Surface Area in Toddlers/Children It should be preserving total surface area. Can you send your mris_preproc command line and the terminal output? It might be something with 5.1 as well. On 8/9/18 3:49 PM, Derek Sayre Andrews wrote: * External Email - Use Caution * Dear Freesurfer Developers and Experts, I have been exploring various vertex wise (mass univariate) effects using freesurfer measures of cortical thickness and surface area in a cohort of toddlers/children aged 25-70 months. When looking at the effect of age on surface area using individuals’ measures mapped to fsaverage and smoothed at 15mm fwhm (area.pial. fwhm15.fsaverage.mgh) I observed a widespread negative effect of age (i.e. decreased surface area with age). Given the age group of the cohort this seems implausible. Plotting the sum of each individuals lh+rh.area.pialfsaverage.fwhm15.mgh against age shows the relationship: cid:image001.png@01D42FCE.C197B360 However, plotting the lh+rh total surface area returned by mris_anatomical_stats reveals a much more plausible relationship between surface area and age: cid:image002.png@01D42FCE.C197B360 My working hypothesis is that the significantly smaller brain sizes of our cohort compared to fsaverage, and the fact(?) that -qcache does not preserve global surface area, is causing an “over adjustment” in our cohorts smallest brains when mapped to fsaverage. Thus, my questions are three fold 1. Is the mapping of our significantly smaller brains to fsaverage a potential explanation for the results we are seeing in our mass univariate analyses of surface area? 2. If this is the case, would this effect be limited to surface area or also extend to other freesurfer measures including cortical thickness, lGI, sulcal depth etc. 3. How would you recommend approaching vertex wise analyses in a cohort of this age? Create a study specific average subject using make_average_subject to map onto? Thank you for your insight and guidance! Best, Derek PS: All processing was performed using freesurfer v5.1 cid:image003.png@01D42FCE.C197B360 *Derek Sayre Andrews, PhD* Postdoctoral Scholar Department of Psychiatry and Behavioral Sciences The M.I.N.D Institute University of California Davis Telephone: +1 916 703 0360 Email: dandrews@UCDavis.edu <mailto:dandrews@UCDavis.edu> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
