[Freesurfer] FMRI group analysis in common surface space

Hi all, We want to perform a FMRI group analysis in common surface space. For that purpose, can we (1) run feat2surf on both cope and varcopes on first-level feat analysis (2) run higher-level feat on the output (using the transformed copes/varcopes as the inputs)? Thanks, Georg _

[Freesurfer] cluster summary to MNI standard space

Hi, I'd like to extract %BOLD-change from clusters or highly activated voxels (first level fMRI data processed in FEAT, higher level done with mri_glmfit). Can you tell me what kind of space the cluster summary list created by mri_surfcluster refers to? Is it real Talairach space as TalX, TalY an

[Freesurfer] reg-feat2anat basics

Hi Doug! May be a very basic question for better understanding, but how much does reg-feat2anat care about the FSL preprocessing e.g. dewarping? And especially important for me, does it make a difference if you FNIRT or FLIRT on first level? Is it a good idea to process non-linearly registered sub

[Freesurfer] mri_glmfit and dofs

Hi Doug! When performing surface-based group analysis with mri_glmfit, I have to specify the dofs of my feat runs. But when I correct for motion outliers on first level (by additional confound EVs identified by fsl_motion_outliers) there will be different dofs for every subject. Is a correct group

AW: [Freesurfer] Registering FSL Feat output to the anatomical

: Georg Homola Cc: 'freesurfer' Betreff: Re: [Freesurfer] Registering FSL Feat output to the anatomical Sorry, this one got lost. Those are "electronic fiducials" placed in the image near the col,row,slice=0. It is for helping you assess whether you have a left-right reversal.

[Freesurfer] mri_glmfit-sim bug?

Hi All (and especially Doug, again)! As one of the final steps I run mri_glmfit-sim for clusterwise correction (of my random effects analysis btw.). It always worked well and I also didn't change the command line recently, but since I updated Freesurfer to the latest version (4.3.1) it quits with:

AW: [Freesurfer] mri_glmfit-sim bug?

ag, 1. Juni 2009 01:46 An: Georg Homola Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] mri_glmfit-sim bug? Is this for a permutation test? Sorry, this is my fault. I've put a new version here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim that shou

Re: [Freesurfer] fsaverage across versions

Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcella

Re: [Freesurfer] fsaverage across versions

Georg Homola Gesendet: Mittwoch, 1. Juli 2009 17:05 An: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] fsaverage across versions Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the o

[Freesurfer] Three classes and GLM

Hi all, I'm having some problems getting a second level fixed effects analysis started on my subjects. There are three runs (dofsum = 884) in each case I'd like to compare. OSGM works fine so far, but when I apply a matrix like this: 1 0 0 0 1 0 0 0 1 To a contrast like that: 0.5 0.5 -1 mri_g

AW: [Freesurfer] Three classes and GLM

uts of the same or different subjects. Or am I totally off the track? Any comments would be appreciated! Thanks again, Georg -Ursprüngliche Nachricht- Von: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Georg Homola Gesendet: Freitag

Re: [Freesurfer] Three classes and GLM / mri_glmfit dof bug

urfer-boun...@nmr.mgh.harvard.edu] Im Auftrag von Douglas N Greve Gesendet: Freitag, 17. Juli 2009 20:04 An: Georg Homola Cc: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] Three classes and GLM This is a bug in mri_glmfit in that it does not recognize that the dof is really 884 and not 0. The

Re: [Freesurfer] Three classes and GLM / mri_glmfit dof bug

org -Ursprüngliche Nachricht- Von: Douglas N Greve [mailto:gr...@nmr.mgh.harvard.edu] Gesendet: Montag, 20. Juli 2009 21:10 An: Georg Homola Cc: 'Freesurfer Mailing List' Betreff: Re: [Freesurfer] Three classes and GLM / mri_glmfit dof bug It probably won't change it tha

[Freesurfer] mri_glmfit reference

Hi, following these refs I've found on the list and the mri_glmfit help, I assume the cluster-wise probability of the permutation simulation is based on cluster mass inference, is that right? Thanks, Georg Statistical Science 2004, Vol. 19, No. 4, 676-685 Institute of Mathematical Statistics,

[Freesurfer] CUDA vs. ATI Stream / OpenCL

Hi Nick (and others), do you already have positive experience with ATI cards, too? We think about buying a new workstation with lots of GPU power so it would be great help to know what really pays off: GeForce GTX 480 or ATI Radeon HD 5870? Or should we go for Nvidia Tesla? What kind of tech specs

Re: [Freesurfer] CUDA vs. ATI Stream / OpenCL

Junior [mailto:p...@netfilter.com.br] Gesendet: Montag, 23. August 2010 00:08 An: Georg Homola Cc: freesurfer@nmr.mgh.harvard.edu Betreff: Re: [Freesurfer] CUDA vs. ATI Stream / OpenCL CUDA won't work on ATI. - Pedro

Re: [Freesurfer] Notes on CUDA Acceleration

Hi Richard and others, allow me one additional remark that may be crucial for those considering to invest in new cards. Although the Fermi class cards make use of the same architecture (Geforce GTX 480 and Tesla C2050 for example), for consumer products (GTX 400 series), double precision performan