[Freesurfer] about labels

hi eveyone     i am quite new in freesurfer, is it possible to generate aparc.a2009s+aseg.mgz from aparc.a2005s+aseg.mgz without re running recon-all thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Surface-based cortical volume calculation

Hi! Ok! That would be a good improvement :) Thanks to both! Cheers, Andreia Citando Douglas N Greve gr...@nmr.mgh.harvard.edu: Actually, you are right! Most of the non-gray matter structures in the medial wall are zeroed out, but the part that goes through the hippo and amygdala are

Re: [Freesurfer] about labels

you can rerun just that step in recon-all, but you won't really be making it from 2005s, just recreating the 2009 parcellation from scratch (which is only a couple of minutes). On Fri, 23 Dec 2011, LAOUCHEDI MAKHLOUF wrote: hi eveyone     i am quite new in freesurfer, is it

[Freesurfer] GLM question

Hello group, I am a new user of Freesurfer and just learning to process data through the pipeline. Sorry if this is an amateur question. I was just trying to look at cortical thickness differences between a patient group and a control group. So, my fsgd file would just list the input

Re: [Freesurfer] GLM question

Hi Koushik, it's very hard to diagnose these problems with out more detailed information (eg, the command line, the FSGD file, and the contrast). Send those along and I'll see if I can figure out what went wrong. doug Govindarajan, Koushik Athreya wrote: Hello group, I am a new

Re: [Freesurfer] GLM question

Many Thanks Doug for the reply. I figured out what the problem was. It was a trivial issue. I had an empty line after my contrasts in my text file and that tripped me off. I was basically practicing doing GLM and was following the pipeline flow exactly but with my data. Regards Koushik

[Freesurfer] Noise filtering before recon-all

We have some T1 images that are kind of noisy that were acquired several years ago. We applied a noise-reduction filter (FSL's SUSAN) to the T1 images before beginning the recon-all segmentation process. Is there any reason not to do this type of smoothing before recon-all, or is there any option

Re: [Freesurfer] Noise filtering before recon-all

Hi Courtney it's hard for us to say, except to try it and visually inspect the results. Check with the Oxford crew as they may have tried this already Bruce On Fri, 23 Dec 2011, Courtney Haswell wrote: We have some T1 images that are kind of noisy that were acquired several years ago. We

Re: [Freesurfer] Tracula - bedpost failure

Hi Kiely - It's strange that bepostx would create ph2samples and not ph1samples. These are the orientation angles for the 2 anisotropic compartments, so if there's a 2nd there should be a 1st. Have you asked about it on the FSL list? a.y On Thu, 22 Dec 2011, Kiely Donnelly wrote: Hi