Re: [Freesurfer] Reviewer request

Hi Jürgen in some ways you can think of it as a partial volume correction. We know the cortex is smooth at the spatial scale of a couple of mm, and so impose this constraint to estimate the location of the surface with subvoxel accuracy. In addition, if a given voxel is darker than it's neigh

Re: [Freesurfer] Segmentation Problem

Hi Markus can you send us an example of where you think the volume is far too low? Tar and gzip the entire subject dir and put it on our filedrop cheers Bruce On Thu, 5 Jan 2012, Markus Savli wrote: > Dear Freesurfer Community! > Recently I started working with Freesurfer and had a number of s

Re: [Freesurfer] SPGR gadolinium contrast

Hi Catherine, yes, we have run post-enhancement datasets through FS with few problems. The only inaccuracies are in the choroid and dura which are a lot brighter than we expect them to be. Still, it typically works fine. cheers Bruce p.s. what do you mean by compressed? On Thu, 5 Jan 2012,

Re: [Freesurfer] SPGR compressed files

Hi Catherine can you explain what you mean by compression? Bruce On Fri, 6 Jan 2012, Cat Chong wrote: > Hi Experts, > > We wanted to run clinical scans that underwent some compression at the > scanner through freesurfer. > I just wanted to seek confirmation that SPGR sequences that have under

[Freesurfer] Group Analysis for non-FA data

Dear Lilla, I wonder if I can use my results from the mri_cvs_register to do a non_FA group study analysis, more exactly I am interested on the mean diffusivity (adc.nii from dt_recon). I hope I don't need to run again the registration again. Since from the significant map I can only find/ tell

[Freesurfer] Building from source without GUIs

I'm attempting to build the development branch of the source code. To reduce dependencies, I'm trying to build without any of the GUI support using the flags: --disable-all-apps --disable-gl-apps It's complaining about a missing dependency: configure: error: FATAL: libBLT not found. Check conf

[Freesurfer] SPGR compressed files

Hi Experts, We wanted to run clinical scans that underwent some compression at the scanner through freesurfer. I just wanted to seek confirmation that SPGR sequences that have undergone slight compression can not be run through freesurfer, is that correct? thank you, catherine

Re: [Freesurfer] GLM design question

Hi Doug, Thanks for your reply again. It's getting more and more clear now. I've however one question remaining, which is regarding the correction for sex. What I did not tell (my fault ;-) ), is that 75% of the cohort is female. Comparing the sex-corrected results with male-only and female-only