[Freesurfer] Fwd: sign mc-z

Dear all, A beginners question: what does the sign mean in the multiple comparison simulations? I thought it defines the side of the t-test performed on the glm parameter estimates, but since you can run the simulations for a bunch of contrasts simultaneously and since in some cases you might be

[Freesurfer] question about voxel size

Hi, I'm looking at a aparc.stats file. I noticed that VoxelVolume is 1 mm^3. However for this patient the voxel size was 0.9 x 0.9 x 1 mm^3 in acquisition. Actually, in the aparc.stats file Nvoxel = Volume_mm3 for each structure. I would like to understand whether the voxel size was resized from

[Freesurfer] Error during file browsing

Hello, I am running FreeSurfer v5.0.0. When in tkSurfer, when I am loading any file, I come across a problem when I press Browse to search for the file. In the Filter bar, the pathway is always followed by */* . There are no files listed in the window below unless I delete the */*. This happens

Re: [Freesurfer] question about voxel size

Hi Roberto all stats should correctly account for the interpolation to 1mm isotropic, so I don't think that's the answer. Did you check the talairach.xfm? It is the basis of the estimated ICV. If it's wrong, so will the ICV be. cheers Bruce On Thu, 19 May 2011, Sghedoni Roberto wrote:

Re: [Freesurfer] recon-all tutorial data

Hi Gabriel, I am not sure if this is precisely the sample data you are looking for, but I found something that resembles a sample data set at /autofs/cluster/freesurfer/subjects --Camilo On May 18, 2011, at 10:11 PM, obre...@nmr.mgh.harvard.edu wrote: Hi, I'm new to the software and I'm

Re: [Freesurfer] Fwd: sign mc-z

Hi Rene, you have the right interpretation for the sign. When you run the correction, it will be applied to all contrasts whether you want it or not. If you want a different sign, then run the correction a second time (it will create new files with new names so you don't overwrite). doug René

Re: [Freesurfer] recon-all tutorial data

Hi Camilo and Gabriel we are regenerating the tutorials to match the upcoming 5.1 release. They should be back up within a week. cheers Bruce On Thu, 19 May 2011, Camilo Lamus wrote: Hi Gabriel, I am not sure if this is precisely the sample data you are looking for, but I found something

[Freesurfer] error message from fast_selxavg.m

Hi, I was running selxavg-sess, and met this error: $Id: fast_selxavg.m,v 1.40.2.2 2009/04/09 20:01:57 greve Exp $ Parsing Arguments RescaleTarget = 1000 UseMRIread = 1, ext = nii Checking Parameters ??? Undefined function or variable xyzscale. Error in == load_nifti_hdr at 138

[Freesurfer] little bug in mri_cvs_register

running mri_cvs_register --mov 004 --template 003 get error executing surf2vol at /apps/x86_64_sci5/freesurfer-latest/bin/elastic_registration_CVS.pl line 162. line 162 is system($cmdLine)==0 or die error executing surf2vol; i saw martin kavec posted the same error but did not see a

Re: [Freesurfer] little bug in mri_cvs_register

Hi Greg, Thanks for your note. I actually got rid of the perl script already so in 5.1 it should not be a problem any more. Lilla On Thu, 19 May 2011, GREGORY R KIRK wrote: running mri_cvs_register --mov 004 --template 003 get error executing surf2vol at

[Freesurfer] ROI analysis in freesurfer

We have a  functional image (beta weights generated in SPM and the original BOLD timeseries they came from ) and a structural image.  We have flattened the anatomical image using freesurfer and have determined some ROIs based on that (retinotopy).  Now we need to apply those ROIs to our BOLD