[Freesurfer] When/What to edit?

Hello FS experts, I have had a continuing curiosity regarding when/what to edit in FS cortical reconstructions. The wiki does a good job at showing how to deal with large scale problems, (i.e. invalid tal transformation, white matter not being recognized, large portions of the skull included in

Re: [Freesurfer] using multiple cores

Hi Bruce! Thanks for the fast response. I used the current stable version 5.3.0.1 (freesurfer-Darwin-lion-stable-pub-v5.3.0.1). So I will try as you have suggested ... Best wishes, Lukas Bruce Fischl Fri, 02 May 2014 05:47:26 -0700 Hi Luke what version of FS are you running? We see

[Freesurfer] effect size for conjunction analyses?

Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation how to display effect sizes for this kind of analyses? Would you show the effect size estimate corresponding to the p-value that is chosen, an average, or

[Freesurfer] MICCAI PC workshop -- May 16 (fwd)

FYI -- Forwarded message -- Date: Fri, 2 May 2014 11:28:11 -0400 From: Polina Golland pol...@csail.mit.edu To: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: MICCAI PC workshop -- May 16 Hi Bruce, Can you please forward this around? Thanks, Polina. MICCAI PC Workshop

[Freesurfer] Fwd: Optseq2: ntp

Dear Douglas, I would like to use optseq2 to set up my experiment sequence. However it is not clear for me what “number of time points” means. I guessed that it was the number a waveform is sampled, but I saw in some mailing lists that it is the time the event is repeated during the run. In case

Re: [Freesurfer] using multiple cores

Hi Bruce!I just run: recon-all -s ernie2 -autorecon2 -openmp 4 mri_ca_register uses 100.9% CPU at most ... Any idea? Should I try to recompile FS for the current MacOS release? If so, do I have to take care on special librariwa in order to enable the openmp option? Best wishes,LukasHi Bruce!

Re: [Freesurfer] using multiple cores

Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014, lukas.sch...@ukb.uni-bonn.de wrote: Hi Bruce! I just run: recon-all -s ernie2  -autorecon2 -openmp 4 mri_ca_register  uses 100.9% CPU

Re: [Freesurfer] using multiple cores

If you are compiling with clang openmp might not work. Peace, Matt. On 5/2/14, 2:13 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Lukas sorry, I'm out of my depth on the mac. Perhaps Zeke knows what's going on? Does OpenMP have to be enabled somehow? Bruce On Fri, 2 May 2014,

Re: [Freesurfer] Fwd: Optseq2: ntp

It is the number of samples in the time series. Eg, if you scan for 10min with a TR=2, then you would have 600/2=300 time points doug On 5/2/14 3:07 PM, Conchy PF wrote: Dear Douglas, I would like to use optseq2 to set up my experiment sequence. However it is not clear for me what number

Re: [Freesurfer] effect size for conjunction analyses?

Hmmm, I'm not sure an effect size makes sense. I guess I would use the one from the chosen p-value doug On 5/2/14 12:52 PM, Caspar M. Schwiedrzik wrote: Hi! I am doing some conjunction analyses (Nichols et al.) on my fMRI data, and I was wondering whether anyone can make a recommendation

[Freesurfer] FSGD and contrast files for group analysis

Dear Marie,I want to run a group analysis on a set of subjects, correcting for gender(Male/Female), diagnois regarding epilepsy (no focus/focus in rh/focus inlh/focus in both h), age and IQ. Should my FSGD file look somewhat like thisbelow:GroupDescriptorFile 2Class NoFocus_MaleClass

Re: [Freesurfer] FSGD and contrast files for group analysis

The FSGD looks right (you have a 2x4 design, so 8 classes, plus 2 covariates). [1 1 -1 0 0 -1 0 0 0 0 0 0 0 0 0 0] tests for a difference between NoFocus and RhFocus (No-RH) [0 0 1 -1 0 1 -1 0 0 0 0 0 0 0 0 0] tests for a difference between RhFocus and LhFocus (RH-RH) probably you

Re: [Freesurfer] brain.finalsurfs.mgz editing

Hi Khadka, Although it is an old mail (sorry), because this topic came up in another thread, I reply here also. You need to edit the brain.finalsurfs.manedit.mgz file. Create this file by copying : cp brain.finalsurfs.mgz brain.finalsurfs.manedit.mgz then edit the manedit file. Best, Martin

Re: [Freesurfer] brain.finalsurfs.manedit.mgz file edits longitudinal processing

Hi Doug, so you 1. edited the cross sectionals and surfaces look fine (make sure you edit the brain.finalsurfs.manedit.mgz file, which you create as a copy of the brain.finalsurfs.mgz) 2. checked/edited the base and surfaces look fine too 3. ran the longitudinal from scratch (w/o any edits)