[Freesurfer] extracting cluster stats from qdec output

I'm trying to extract thickness, area and volume stats from individual subjects using clusters generated from a qdec analysis. The command I'm using is: mris_anatomical_stats -a /Users/flalonde/Desktop/WAGR_freesurfer5.3/qdec/Untitled/lh-Diff-HV-PAX6-Intercept-area/mc-z.abs.th20.sig.ocn.annot

[Freesurfer] extracting cluster surface area measurements for individual subjects from qdec output

I’m trying to extract the surface area measurements for each subject from clusters generated by Monte Carlo analysis within qdec. From previous posts I came up with the following command: mri_segstats --annot fsaverage lh mc-z.abs.th20.sig.ocn --i y.mgh --avgwf lh-Diff-HV-WAGR-Intercept-area.d

[Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

I am following the wiki page for LME analysis and I have a quick question. The Mass-univariate example near the bottom of the page proposes an initial model that contains intercept, linear and quadratic terms as random effects. However, the examples just below for lme_mass_fit_EM_init(), lme

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

dinal mass-univariate analyses with lme (hopefully soon). Best -Jorge ________________ De: "Lalonde, Francois (NIH/NIMH) [E]" mailto:flalo...@mail.nih.gov>> Para: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:frees

Re: [Freesurfer] specifying random effects in LME (Linear Mixed Effects models)

and unbiased estimation of the between-subject variability. Best -Jorge ________________ De: "Lalonde, Francois (NIH/NIMH) [E]" mailto:flalo...@mail.nih.gov>> Para: "freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu>" mailto:fr

[Freesurfer] non-parallel version of LME models MATLAB scripts

In running a mass-univariate LME models analysis I keep running into calls to the parallel computing toolbox (parfor, matlabpool, etc…). I was able to comment out these lines in some of the scripts but I've run up to one that is particularly difficult to modify (I am not an expert in MATLAB).

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

e, Douglas N.,Ph.D." wrote: Not sure. Can you tar up the subject and send me the file here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming? Let me know when it is transferred. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > >

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

the README. I ran it on your data, and it looks pretty good. On 1/22/19 12:03 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > > External Email - Use Caution > > Hi, > > We collected an MP-RAGE scan at .6mm isotropic resolution with the

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

The dev version has the same problem :( On 1/24/19 6:37 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > The data I sent was generated using the development version, freesurfer-linux-centos7_x86_64

Re: [Freesurfer] Errors in white matter surfaces from scan collected on 3T Siemens Skyra scanner at .6 mm resolution

Is this correct? Thanks, François On 2/5/19, 12:41 PM, "Greve, Douglas N.,Ph.D." wrote: good to hear! On 2/5/19 12:19 PM, Lalonde, Francois (NIH/NIMH) [E] wrote: > External Email - Use Caution > > Hi Doug, > > Sorry for the delay i