What was your exact mri_segstats command?
On 11/15/2016 05:59 PM, Elijah Mak wrote: > 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> > <mailto: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 > <mailto:Freesurfer@nmr.mgh.harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- > Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu > <mailto:gr...@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: > 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: > https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > 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 > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@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/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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 . 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