New subject: Extracting structural measures from trend-level PET clusters

15 Nov 2016

      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

Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- 
Douglas N. Greve, Ph.D.
MGH-NMR Centergr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2www.nmr.mgh.harvard.edu/facility/f...
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

*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
 Wed, 09 Nov 2016 13:22:06 -0800
http://www.mail-archive.com/search?l=freesurfer@nmr.mgh.harvard.edu&q=date:20161109

You can just

mri_segstats --i thickness.stack.mgh --seg cache.th30.pos.sig.ocn.nii.gz

--excludeid 0 --avgwf thickness.stack.cluster.dat

Each row in thickness.stack.cluster.dat will be a subject, and each

column is a cluster

On 11/09/2016 04:16 PM, Elijah Mak wrote:

> Hi Freesurfer Team,

>

> 1) We've found some subtle differences in tau accumulation between two

> groups. Unfortunately, it does not survive mri_glmfit-sim (voxel

> threshold 0.001, cwp < 0.05). Still, I would like to extract the

> structural measures from the uncorrected tau clusters (p<0.001). What

> is the most convenient approach for this?

>

> Could the following URL

> (http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html

> http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg16268.html

> ) be a solution? Can mri_label2label work for sig.mgh with multiple

> clusters?

>

> 2) A slightly unrelated question: how can I go about using this

> particular cluster as a seed for functional or tractography analysis

> in other softwares (i.e. FSL or MRTRIX) or even within Freesurfer if

> possible?

>

> Thanks again. Really appreciate your help

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