[Freesurfer] FS 6

Dear fs experts, Is there a version of fs 6 for Windows to download. Thank u John On Tuesday, March 8, 2016, Bruce Fischl wrote: > Hi David > > I'm pretty sure that the Wash U HCP group has sorted this out. Have you > asked them? > > cheers > Bruce > > > On Tue, 8 Mar 2016, Slater David wrote: >

Re: [Freesurfer] FS 6

Hi John there is no version 6 yet, so no! Our windows support will be the same as previously though when it is ready - a virtual box version I believe. cheers Bruce On Fri, 11 Mar 2016, John Epiktitos wrote: Dear fs experts,Is there a version of fs 6 for Windows to download. Thank u John O

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

Hi Martin, Thanks for the answer :-) To presmooth the data onto target, with the following command: recon-all -long -qcache The , does that have to be the longitudinal name (d115a.long.d115_base) or the cross-sectional name (d115a)? Best wishes Kasper 2016-03-09 22:38 GMT+01:00 Martin Reute

[Freesurfer] For Monte Carlo simulation, QDEC GUI or in-line command?

Dear Freesurfer Experts: I repost a question I have when applying Monte Carlo simulation to control for multiple comparisons. Your help is much appreciated. I did the correction via QDEC GUI. In the section of Monte Carlo Null-Z simulation, I set Threshold: 2.0 (0.01) and Sign: neg. This

[Freesurfer] Alpha channel in color lookup tables (CLUT)

Dear Freesurfer community, I have a problem using the alpha channel in the color lookup tables. No matter what values I choose, none of them seem to affect the transparency in any way. Here is what I would like to do: I have a number of labels that I want to visualize on an inflated brain surface

[Freesurfer] mri_glmfit

Hi FS experts, I am trying to run OSGM analysis between two groups using mri_glmfit as follow : mri_glmfit --y lh_10mm.mgh --fsgd fsgd.dat --glmdir lh_10mm --surf fsaverage lh --osgm    it keep returning as: ERROR: DOF = 0   my FSGD is as follow  GroupDescriptorFile 1 Title OSGM Class group1

[Freesurfer] Difficulty correcting Pial surfaces

Dear FS experts.I am having issues when trying to remove non cortical tissue (mostly skull). I load my images as follow: freeview -v mri/T1.mgz mri/brainmask.mgz -f surf/lh.white:edgecolor=yellow surf/lh.pial:edgecolor=red surf/rh.white:edgecolor=yellow surf/rh.pial:edgecolor=r Then I hav

Re: [Freesurfer] Cross sectional analysis of a longitudinal data

Hi Kasper, That needs to be the cross-sectinal name (whenever you also pass a base, it will automatically create the ..long.. names internally). cheers, Martin On 03/11/2016 08:51 AM, Kasper Jessen wrote: Hi Martin, Thanks for the answer :-) To presmooth the data onto target, with the fol

[Freesurfer] FA maps surface based analysis

Hi FS experts, How can ai do surface based analysis on FA maps. In other wods: I have 20 subjects( two groups 10/10) and FA map for every subject. How can I dtufy the differnce between the groups in FA on surface?   Best, John ___ Freesurfer mailing l

Re: [Freesurfer] Fsaverage

I don't know that it has really been tested. The registration is surface-based so it will be much less sensitive to different gross anatomy than volume-based methods. On 03/09/2016 11:37 AM, Kasper Jessen wrote: > Dear FreeSurfer experts, > > In regard to fsaverage, we are wondering whether it i

Re: [Freesurfer] selxavg3-sess question

Yes, it is. I forgot that version 5.3 uses the brain mask from the first run. This is fixed in version 6. On 03/09/2016 02:42 PM, Ji Won Bang wrote: > Dear. Freesurfer experts. > > Hi. > > I'm pretty sure that this error is due to the different number of > slices in different runs > > I ran

Re: [Freesurfer] Using qdec to view cluster results

Hi Sahil, that functionality was never fully developed in QDEC so we are recommending that people only visualize their uncorrected results in QDEC. For doing the full analysis, you can run QDEC to decide which factors you want to use in the model (and have it generate an FSGD file), but then us

Re: [Freesurfer] unknown option in new brainstem segmentation

I think that must have been a bug introduced into recon-all just before you downloaded the development version. It is not there in the current dev. Part of the danger when using the dev version. On 03/11/2016 07:00 AM, Claudia Testa wrote: > Hi Douglas > > sure. Let me know if you need any other

[Freesurfer] Freesurfer v6 beta

Hi folks, I was just wondering if there was any major bug in the freesurfer v6 beta that necessitated the removal of the beta from your servers because I cannot find them anymore. Does that mean I will have to go with the dev version at this point which are like the nightlies of the freesurfer v6

Re: [Freesurfer] Freesurfer v6 beta

Indeed the v6.0 beta was removed,,, not because of a "major" bug but rather it was just decided that significant development was still needed before a true beta could be released. We continue to make improvements and will be releasing a v6 beta soon, but at this point if you want the latest ver