Re: [Freesurfer] Fw: longitudinal statistics LGI

2015-03-30 Thread amirhossein manzouri
Dear Jorge, Thanks for the reply , when I run *lhstats1 = lme_mass_fit_vw(X, [1 2], lhY, ni, lhcortex); *Matlab says that it doesn't converge in 99% ! Another question is about the approach you suggested in the FreeSurfer website, [lhTh0,lhRe] = lme_mass_fit_EMinit(X,[1 2],Y,ni,lhcortex,3);

[Freesurfer] TRACULA_SNR

2015-03-30 Thread Alshikho, Mohamad J.
Hi Anastasia, dwi_snr.txt is an output of the preprocessing step in TRACULA. Kindly how TRACULA is calculating the SNR for every direction in DTI data? Is there any command line that can do it? Thanks, Mohamad ___ Freesurfer mailing list

Re: [Freesurfer] Tracula: cannot open file `1000' for reading Bedpost file error

2015-03-30 Thread Katherine Damme
Hello Anastasia, I did specify the files. I used the same config file (attached) a few months ago to write make a tracula image and then the dpath was deleted by mistake and when I tried to rerun the same file it is giving me this error. On Fri, Mar 6, 2015 at 6:07 PM, Anastasia Yendiki

[Freesurfer] longitudinal

2015-03-30 Thread Kate Riggall
Hello all, I am running a 2 time point longitudinal analysis of some structural brain images. I have noticed that there is some issues with the cortical surface reconstruction, i.e. some grey matter not recognised etc. As this is a short project, I do not have time to fix each image manually, but