Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Matthieu, replacing time by score is very different from adding score as a covariate. Often scores are crude and often they are constant in controls (always full score), and only vary slightly in diseased. In those cases it may not be good to use score as a time variable. I would either a

Re: [Freesurfer] long_stats results for group analysis

Hi Maria, That command creates a stack of the percent changes , with one entry per subject (it reduces the longitudinal data of a subject to a single number, e.g. the percent change computed in different ways). Make sure you know what the difference is between pc1, pc1fit (in your case this

[Freesurfer] ERROR: must specify input table of b-values

Hello, I am trying to run the trac-all -prep command in TRACULA on a participant. However, every time I run the command trac-prepoc exits with errors and I get the message: 'ERROR:must specify input table of b-values'. I checked over the configuration file and everything seems correct: b-value

[Freesurfer] Posting to Freesurfer

Hello, I just subscribed to Freesurfer and I would like to be able to post to the list. My email is herring...@osu.edu Thanks, Elizabeth Herring ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listin

[Freesurfer] Research Assistant Position in Clinical Neuroscience Laboratory

Research Assistant Position Clinical Neuroscience Laboratory Department of Psychology Ohio State University Applications are being sought for a full-time research assistant position, starting June 1st, 2017, in the Clinical Neuroscience Laboratory

[Freesurfer] Mean gray-white contrast for each ROI

Hi, I read from a previous post that the "{lh,rh}.w-g.pct.stats files in $SUBJECTS_DIR/subject/stats … will have the mean gray-white contrast for each ROI in the aparc." I've looked at the lh.w-g.pct.stats file and am not sure which values I should be looking at if I am interested in the ratio

Re: [Freesurfer] Question of longitudinal processing

Hi Martin, Thanks a lot. It had worked nicely. I got one question about this following cmd tksurfer fsaverage lh pial -overlay lh.testretest.thickness-pc1.fwhm15/osgm/sig.mgh I got a red to yellow sig.mgh, does it mean I got a increased percent thickness change (pc1)? and the color bar showing 2

Re: [Freesurfer] LME : longitudinal correlations between imaging and cognition scores

Hi Martin, I will read up on interpretation of time varying covariates. If initially I use score as variable fixed across time, and define a variable for 'score x time' interaction: 1) Would putting only 1 to 'score x time' column (for contrast) test for progression of correlation patterns betwee

[Freesurfer] longitudinal analysis or cross-sectional anslysis of the subfield of hippocampus

Dear all, I have 2 groups (patients and controls), and I want to analysis the subfields of the hippocampus. Some of the subjects have 2 scans (before treatment and post treatment) and some subjects only have one scan(before treatment). aim 1: I want to compare the subfied volume of the hippocampus

[Freesurfer] -usegpu vs -parallel in recon-all

Dear All, With FS6, -parallel -openmp x can really speed things up. I inherited code from prior versions using -usegpu flag for GPU/CUDA (not supported more recently). Is the latter redundant or affecting in any way the -parallel -openmp x performance, should we take it out, please advise. Thank

Re: [Freesurfer] Question of longitudinal processing

Hi Jahanvi, I think red is positive (some people invert the colors, then red=hot=dangerous ). But I think default is blue negative, red positive, so there is an average increase in thickness. You should also look at the effect size (gamma). The p -values are in log 10 space, so 2 = 0.01 and 5

Re: [Freesurfer] Question of longitudinal processing

Hi Martin, Thanks a lot for the reply. Is there a way to display the bar in effect size? And is this sig.mgh already statistically corrected? (FDR?) Best, Jahanvi On Thu, May 18, 2017 at 1:55 AM, Martin Reuter wrote: > Hi Jahanvi, > > I think red is positive (some people invert the colors, the