Re: [Freesurfer] Recon-all Error

Hi Esha, this is not how you setup a freesurfer call. What you did is create a single subjects with 1000 scans and the motion correction step tries to average all these scans into a single file. Instead you need to create for each subject a directory and put the corresponding file there: 001/mr

Re: [Freesurfer] tksurfer tool "graph marked vertices avg" not active

The next step would be to do a correlation between symptom severity and the clustering. Therefore, I want to do a ROI extraction. The aim is to see whether the severity of symptoms correlates with the degree of the structural brain alterations found. 2014-08-09 21:05 GMT+02:00 Katharina Zech : >

Re: [Freesurfer] insula on medial surface

Hi Michael, I looked at the 2 subjects you sent me : the insula label of the aparc/aseg parcellation is obviously too large : it includes the insula, the limen insulae and, from there it propagates to the anterior perforated space, just posterior to the orbital gyri, to join the subcallosal ar

Re: [Freesurfer] Checking Back In: FLAIR Registration Problems

Good afternoon, I'm just checking in about a bbregister problem I emailed about last week (see email chain below). Thank you very much! Marta Zamroziewicz MD/PhD Candidate Decision Neuroscience Laboratory University of Illinois Urbana-Champaign mzam...@illinois.edu

[Freesurfer] What is the best method to calculate cohenD or any other map of effective size with lme?

Dear FreeSurfer expert I have calculated the residuals as y-x*beta as described in (Bernal-Rusiel et al., 2012). What is the best method to calculate cohenD or any other map of effective size with lme? Can I calculate cohenD as R=y-desingmatrix*Bhat cohenD=gamma./(sqrt(sum(r.^2)/df2-1)) Ref