Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

Hi Doug,

I am not sure if this is the correct way to reply to the thread. I thought that adding a "RE:" in front of the subject would automatically link the email to its orginal thread. I hope this works!

I am pasting the previous emails below.

Thanks again, Doug.

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=subject:%22Re%5C%3A+%5C%5BFreesurfer%5C%5D+Extracting+structural+measures+from+trend%5C-level+PET+clusters%22&o=newest

Douglas N Greve http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=from:%22Douglas+N+Greve%22 Mon, 14 Nov 2016 08:07:03 -0800 http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161114

Hi Elijah, can you repost with previous correspondence included? We get a lot of emails here and can't keep track of each person's issue. thanks!

doug

On 11/11/2016 08:06 PM, Elijah Mak wrote:

Hi,

A bit more info: the stack of thickness maps consists of lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I used mri_concat --f --o to create the stack of mghs. I also noticed that the vertex values are in the range of 20-30, whereas those in the lh.thickness.fsvaerage mghs are in the expected range.

Should I be using this for the calculation of the thickness in the clusters instead?

Best Wishes, Elijah

On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak <fk...@medschl.cam.ac.uk <mailto:fk...@medschl.cam.ac.uk fk...@medschl.cam.ac.uk>> wrote:

Thanks, Doug.

It works but I am not sure if the values I'm getting are correct.
Is this supposed to be reporting the mean cortical thickness of
each cluster? I have pasted the output below from the avgwf
below.  The names of the clusters correspond to the regions from
the "summary" text, am I right?


Group     lh_fusiform     lh_precentral   lh_insular      lh_precuneus
lh_parsorbitalis
1         24.29454        29.53935        14.24736        28.97924

31.54577 1 25.68872 28.26156 17.47828 28.20604 30.38902 2 25.46281 30.75879 19.34943 29.59019 32.0404 2 25.55514 27.23871 17.27937 29.14274 29.75657

Another related question: Is it possible to simply take the mean
cortical thickness across the voxels exceeding p<0.001 from the
uncorrected sig.mgh?

Thanks again!

Best Wishes,
Elijah

--

Elijah Mak, Gates Scholar

PhD Candidate *|* Psychiatry

University of Cambridge

Trinity College, Cambridge, CB2 1TQ

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