krista kelly wrote:
Thanks Doug, but would mris_fwhm still be useful if I've already added the -qcache command while running recon all? I have smoothed files in my subjects' surf folders (i.e. lh.area.fwhm15.fsaverage.mgh). I want to extract the smoothed cortical thickness and surface area values for my subjects but am not exactly sure which commands to use.
If you are going to use lh.thickness and your want it to be smoothed, then you will need to smooth it. Pass the smoothed thickness as input to mris_anatomical_stats.
Also, I know that I don't really need to use a smoothing kernel if I'm looking for cortical thickness within certain ROIs (presumably because I'm getting the average), but is this also ok for surface area data? I only ask because I'm not getting an average surface area like I am with cortical thickness, it's the total surface area. So would smoothing be something that I should do for surface area?
For individual ROI area measures, there is no need to smooth (and does not really make sense as you point out).
doug
Thanks!
On Mon, Oct 24, 2011 at 4:06 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
no, that would be 15 "smooth steps". If you want to smooth by 15mm, then use mris_fwhm. doug krista kelly wrote: Would the following code give me data smoothed with 15 fwhm kernel? mris_anatomical_stats -l lh.v1.label -t lh.thickness -nsmooth 15 -b -f BV01/stats/lh.v1_pial.stats BV01 lh pial Thanks! On Mon, Oct 24, 2011 at 10:40 AM, krista kelly <krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com> <mailto:krista.kelly16@gmail.com <mailto:krista.kelly16@gmail.com>>> wrote: Thanks for clearing this up! It makes a lot more sense now. On Mon, Oct 24, 2011 at 10:35 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>> wrote: krista kelly wrote: I'm looking at both cortical thickness and surface area differences between two groups. I've been using mris_anatomical_stats to retrieve values but had a few questions: 1) Do I need to do separate mris_anatomical_stats using different thickness files (bolded below) to get cortical thickness and surface area measures. For example: cortical thickness - mris_anatomical_stats -l lh.v1.label -t *lh.thickness* -b -f BV01/stats/lh.v1.stats BV01 lh surface area - mris_anatomical_stats -l lh.v1.label -t *lh.area *-b -f BV01/stats/lh.v1.stats BV01 lh Or, since the output files include all of these measures, is it fine to just run one of the two? Just run the first one. 2) The output files for both analyses run above (with different thickness files) have identical values for everything except for tray matter volume. Using lh.thickness file - grayvol = 8082; using lh.area file - grayvol = 4029. Can anyone clarify why this happens? It computes the gray matter volume by thickness*area. If you pass it "area" as the "thickness", then you are probably getting area*area. Though I'm surprised that the "thickness" values are correct. 3) The default surface area values are for the white matter surface. How do I run mri_anatomical_stats to get the pial surface? I've tried mris_anatomical_stats -l lh.v1.label -t *lh.area.pial *-b -f BV01/stats/lh.v1.stats BV01 lh but I get identical values for everything (except grayvol). Try adding "pial" to the end of the command line (and use lh.thickness) doug Thanks! Krista ------------------------------------------------------------------------ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> Phone Number: 617-724-2358 <tel:617-724-2358> <tel:617-724-2358 <tel:617-724-2358>> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 <tel:617-726-7422>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> 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. -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>
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