[Freesurfer] Monte Carlos for Volume? (Part 2)

Hello, The mris_preproc command generates a concatenated group surface mgh file for easy use with the monte carlo analysis. Is there such a command to concatenate volume data for use with the monte carlo command for a group analysis? I wrote freesurfer earlier this week asking if you can use the

[Freesurfer] Qdec and error with ?h.aparc.a2005s.thickness

Dear Freesurfers, I get the following error message in Qdec (1.1) when I choose ? h.aparc.a2005s.thickness on the tutorial data: Loading data table /Applications/freesurfer/subjects/qdec/ stats_tables//lh.aparc.a2005s.thickness.stats.dat... Number of columns: 79 fsid column:1 Number

Re: [Freesurfer] FDR correction

Dear Lars, Pedro and all, There should be no problem in using different thresholds for each of these pairwise comparisons. Let's consider the following extreme case: Suppose in one of these comparisons you have a strong effect (say, "activation") that comprises large brain regions. Suppose t

Re: [Freesurfer] FDR correction

Dear Anderson, Thank you for that very thoughtful reply! I think your argument is convicing and I've decided to use FDR for each comparison individually. Lars On Thu, Mar 26, 2009 at 5:37 PM, Anderson Winkler wrote: > Dear Lars, Pedro and all, > > There should be no problem in using different

[Freesurfer] extracting data used in QDEC scatterplots

Hi, I would like to extract the thickness values displayed in the scatterplots in QDEC. Is there an existing method for exporting these values into a text file? Thanks, Sam University of California, Los Angeles ___ Freesurfer mailing list Freesur

Re: [Freesurfer] extracting data used in QDEC scatterplots

Yes. Use the script in UserContributions section of the Wiki http://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/Scripts/ppaulo/qdec-coord --- Pedro Paulo de M. Oliveira Junior Diretor de Operações Netfilter & SpeedComm Telecom --- No

[Freesurfer] recon-all finished with errors

There is a researcher here who is getting this error in version 4.2.0, I have uploaded the 001.mgz to the ftp: TEMPLATE DEFORMATION second estimation of the COG coord: x=150,y=117, z=145, r=8362 iterations GLOBAL CSF_MIN=1, CSF_intensity=2, CSF_MAX=4

Re: Fwd: [Freesurfer] Incorrect correspondence in the aparc+aseg.mgz volume?

Hi Ryan, I still don't quite understand what I'm looking at. Maybe you can put a problem subject somewhere we can get to it? cheers, Bruce On Thu, 26 Mar 2009, Ryan Scotton wrote: For whatever reason, my email from this morning doesn't seem to have gone through. Hopefully it will work t

[Freesurfer] selxavg3-sess error: matrix is singular to working precision

Hello all, I am trying to run a first level analysis on a subject with selxavg3-sess but keep running into the same error. The dof file is created, but that is it. Any ideas what might be causing this? Below is the error given. Thank you very much for your help, Jeremy [jel...@psych118 fun

[Freesurfer] pial.outer.smoothed

Sorry to bother with such a trivial question, but I looked everywhere. How and where is the ?h.pial.outer.smoothed surface created? I understand this surface represents the outer surface of the pial without sulci, similar in shape to the inner surface of the skull. Thanks, Thomas ___