[Freesurfer] local intensity inhomogeneity

Hello freesurfers, We've seen some poor surface reconstructions due to local inhomogeneities that remain in the brainmask volume. We see omission of significant portions of brain tissue due to signal fall off (both gray and white voxels are darker than in surrounding area) that we are unable to

Re: [Freesurfer] LGI and MATLAB

Thanks Bruce. On Fri, Sep 16, 2016 at 2:02 PM, Bruce Fischl wrote: > Hi Alan > > make sure matlab is in your path. You can check by typing: > > > which matlab > > > cheers > Bruce > > On Fri, 16 Sep 2016, Alan Francis wrote: > > Hi Marie - >> >> I have MATLAB and the

[Freesurfer] Freeview error: Surface does not contain valid volume geometry information

Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I get this warning: Surface does not contain valid volume geometry information. It may not align with volumes and other surfaces. What's wrong? I'm using 5.1 version. Thanks to all. Claudia -- Dott.ssa Claudia

Re: [Freesurfer] local intensity inhomogeneity

Hi Jason this is what control points are designed to fix. Why don't they help? Bruce On Tue, 20 Sep 2016, Jason Tourville wrote: > Hello freesurfers,We've seen some poor surface reconstructions due to local > inhomogeneities that remain in the brainmask volume. We see omission of > significant

Re: [Freesurfer] Display FSL PALM(permutation) stats in freeview

Hi Ajay, Make sure you have to run palm_hemisplit on the outputs first, i.e.: palm_hemisplit bh.thickness_* Note that the "-o bh.thickness" was a somewhat poor choice of outputs as now it's necessary to use the underscore ("_") to avoid overwriting original inputs; for future runs, consider

Re: [Freesurfer] Dev builds not found

Thanks! It's working now! On Sunday, September 18, 2016 10:34 PM, Leila Reddy wrote: Hi Bruce,Thanks for your reply. Does anyone on the list have access to the tar file of the latest dev build that they could put on some other site or in a public Dropbox folder? I

[Freesurfer] fmri pipeline

Hi, I am getting a bit confused from the mailing archive on how to properly map volume fmri data into surface fsaverage5. 1. Should I map the volume fmri into individual surface first and then to fsaverage, or I won't loose data if I map it directly to fsaverage5? 2. Should I smooth the data

Re: [Freesurfer] Freeview error: Surface does not contain valid volume geometry information

Hi Claudia you need to send us your full command line and the various other information we ask for when reporting issues (operating system, etc..) thanks Bruce On Tue, 20 Sep 2016, Claudia Dacquino wrote: Hi all, after doing GLM analysis I'm trying to run freeview to see results, but I

Re: [Freesurfer] White matter surface don't change after editing

Hi Cong we are experiencing serious disk problems at Martinos, so the ftp site is down. Try changing the values for mri_segment also. Note that what you are seeing are NOT topological defects as mris_make_surfaces preserves the input topology whatever its settings. Make sure to look in 3D