Hi Derek, sorry for the delay in getting back to you. I'm glad you were able to figure it out ... doug
On 9/18/18 1:29 PM, Andrews, Derek wrote:
External Email - Use Caution Dear Freesurfer Developers and Experts,
Running v6 mris_preproc seems to have solved the issue.
Results of mris_anatomical stats total surface area (best guess at truth in native space): [cid:part1.16B5D076.8EF6E6A3@mgh.harvard.edu] Previous v5.1 recon-all -qcache result: [cid:part2.A1BC0465.97CD1A47@mgh.harvard.edu] V6 mris_preproc result: [cid:part3.BEDF84F3.92DFC19F@mgh.harvard.edu]
Hopefully this may be helpful to someone in the future. Thank you for your support.
Best, Derek
From: "Andrews, Derek" derek.andrews@kcl.ac.ukmailto:derek.andrews@kcl.ac.uk Date: Monday, September 17, 2018 at 11:48 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu, Derek Sayre Andrews dandrews@ucdavis.edumailto:dandrews@ucdavis.edu Subject: Re: [Freesurfer] Surface Area in Toddlers/Children
Dear Freesurfer Developers and Experts,
Professor Greve was able to track the initial error in this thread to an issue with freesurfer v5.1 no preserving global surface area when recon-all -qcache was run for surface area and volume. (i.e. the --jac flag not being turned on when mris_preproc is called).
My first inclination was to move to v6 and simply rerun recon-all -qcache, however this failed due to missing .k files. Which I am assuming are new to v6? I would rerun the entire sample through the recon-all pipeline, however we have over 900 scans that have been processed and meticulously manually edited on v5.1. I fear these edits would be incompatible with v6, making it infeasible to reprocess.
Thus, I moved onto the initial proposed solution of running mris_preproc with the --jac flag specifically on the area.pial and volume surf files. However, the --jac flag is not recognized for the v1.59.2.1 of mris_preproc (2011/05/17) nor is in the comments for v1.76.2.1 that ships with fs v6.
So, I am at a bit of a loss as to how to proceed. A possible workaround the missing .k files to run recon-all -qcache v6 on the v5.1 recons? Something I am missing to get the mris_preproc --jac running?
Any guidance is as always greatly appreciated. Thank you for your valuable time.
Best, Derek
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Sunday, August 12, 2018 at 10:25 AM To: Derek Sayre Andrews dandrews@ucdavis.edumailto:dandrews@ucdavis.edu, free surfer freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Surface Area in Toddlers/Children
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
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.edumailto:dandrews@UCDavis.edu
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Date: Friday, August 10, 2018 at 11:12 AM To: "freesurfer@nmr.mgh.harvard.edu"mailto:freesurfer@nmr.mgh.harvard.edu freesurfer@nmr.mgh.harvard.edumailto: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 SurfStatReadDatahttps://emea01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.math.mcgill.ca%2Fkeith%2Fsurfstat%2F&data=01%7C01%7Cderek.andrews%40kcl.ac.uk%7C8ec8b17164924db0663008d60078968e%7C8370cf1416f34c16b83c724071654356%7C0&sdata=oUYnnB3YxmJ9j4xZufxZC8dP0zFezrVtresCFtzqVWg%3D&reserved=0 and summed them across each vertex.
Would the terminal output of recon-all -qcache be helpful?
Best, Derek
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.edumailto:dandrews@UCDavis.edu
From: freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Douglas Greve dgreve@mgh.harvard.edumailto:dgreve@mgh.harvard.edu Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edumailto: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.edumailto: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?
1. 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.
1. 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
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.edumailto:dandrews@UCDavis.edu
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