Re: [Freesurfer] Talairach transformation

2011-09-09 Thread Bruce Fischl
Hi Maria as long as the tal xform is reasonable I wouldn't worry about it, unless for some reason you care a lot about the accuracy of the talairach coords. cheers Bruce p.s. not sure why it would be smaller On Fri, 9 Sep 2011, Maria Felber wrote: Dear all, sorry, if that question came up

Re: [Freesurfer] Ventricular structures - exact definitions

2011-09-09 Thread Bruce Fischl
Hi Meike sorry for the delayed response. For the ventricular stuff you are probably better off contacting the CMA (Dave Kennedy, Nikos Makris, Verne Caviness). The inf-lat-vent is the part of the ventricle in the medial temporal lobe (the temporal horn), but they could provide a more exact

Re: [Freesurfer] autorecon1 output is just a white block

2011-09-09 Thread Sita Kakunoori
Hi Christopher, If you want to upload the dataset, I can take a look. Sita. On Fri, 9 Sep 2011, Christopher Luna wrote: Hello, After running an *.img file through autorecon1. Freesurfer says it finishes with errors, but I cannot find any error messages in the command line output.

[Freesurfer] bedpostx changes in past 2 years?

2011-09-09 Thread swoodman
Hi all, We always run bedpostx in the developement (nmr-dev-env) environment, and after some digging around, we've noticed some differences in outputs between 2008 and now. Has anything changed with bedpostx in dev environment since 2008, that would effect data and/or analysis? There seem to be

Re: [Freesurfer] bedpostx changes in past 2 years?

2011-09-09 Thread Anastasia Yendiki
Hi Sandra - Bedpost is an FSL program, so your question would be best answered on the FSL list. But yes, I do believe there were changes to it since 2008. For sure there are more outputs saved in the output dir now than before. Not sure if there were changes to the algorithm beyond this. a.y