[Freesurfer] contrast matrix for 2 discrete factors and 3 continuous variables

2011-01-17 Thread Jose Luis Cantero Lorente
- Dear Freesurfers,   My experimental design includes 2 discrete factors and 3 continuous variables:   Discrete factors: -   Diagnosis with three levels (A, B, C) -   Gender with two levels (Males, Females)   Continuous variables: -   Mean cortical

Re: [Freesurfer] two issues with the processing stream

2011-01-17 Thread Nick Schmansky
2. recon-all runs the old fixer 'mris_fix_topology', and if that fails the euler number check, then it runs the new fixer 'mris_topo_fixer'. of course really bad brains fail both. n. On Mon, 2011-01-17 at 13:56 -0500, Bruce Fischl wrote: > Hi Ilana, > > 1. This is usually because of big topologic

Re: [Freesurfer] two issues with the processing stream

2011-01-17 Thread Bruce Fischl
Hi Ilana, 1. This is usually because of big topological defects, in the worst case if the cerebellum or skull are attached. Look at the end of the recon-all.log and see what it is in the middle of doing. If it's topology fixing, check the inflated.nofix file and see if there is a huge defect.

[Freesurfer] two issues with the processing stream

2011-01-17 Thread Ilana Hairston
Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: co

[Freesurfer] two issues with the processing stream

2011-01-17 Thread Ilana Hairston
Hi there, we are having two unrelated problems with a couple of files: 1. A brain running extremely slow, after initial processing. i.e. we ran recon-all, made some edits (control points etc.) and now for some reason the second round is taking days. 2. An error message*: ERROR: _FindFacePath: co

[Freesurfer] mkanalysis-sess -gui

2011-01-17 Thread Iris.steinmann
Hi Freesurfers, I have a little problem: I use a linux mashine with ubuntu 10.10 and installed freesurfer-Linux-rh9-stable-pub-v4.0.5-full.tar.gz.. Most commands are working well (like tkmedit, tksurfer …), but I have a problem to get an analyse gui with (mkanalysis-sess -gui). I just get a long e

[Freesurfer] How to make a surface overlay?

2011-01-17 Thread Ed Gronenschild
Hi, I've done some statistics on thickness and volume of the default cortical regions (segIDs 1000 - 1035 and 2000 - 2035) for a number of subjects. How can I show for instance the p values (expressed as -log(p)) as an overlay on the pial surface of fsaverage? Ed