[Freesurfer] Exporting data from "Find Clusters and Goto Max"

2013-07-06 Thread Sean Hatton
Hi all, Within QDEC, when I click on the "Find Clusters and Goto Max" button I can see the individual thickness values per datapoint. 1. I am co-vaying for age: would these values be raw thickness values or estimated margin means? 2. Considering I have 100s of subjects and several ROIs, how do

Re: [Freesurfer] Error after recon_all on pre-BETed image

2013-07-06 Thread Bruce Fischl
p.s. I think that is a warning embedded in the depths of some open source numerical minimization code we use that seems benign On Sat, 6 Jul 2013, Lin, Richard Lee-Tsong wrote: > Attaching other log outputs from recon-all. Thanks. > > From: freesurfer-bou

Re: [Freesurfer] Error after recon_all on pre-BETed image

2013-07-06 Thread Bruce Fischl
Hi Richard I think that's ok. Run it all the way and see if it works Cheers Bruce On Jul 6, 2013, at 3:35 PM, "Lin, Richard Lee-Tsong" wrote: > Hi FS gurus, > > For whatever reason, BET worked better on my structural image than > mri_watershed, so I used a BET image with recon-all -autoreco

Re: [Freesurfer] Error after recon_all on pre-BETed image

2013-07-06 Thread Lin, Richard Lee-Tsong
Attaching other log outputs from recon-all. Thanks. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Lin, Richard Lee-Tsong [richard_...@hms.harvard.edu] Sent: Saturday, July 06, 2013 3:35 PM To: free surfe

Re: [Freesurfer] freesurfer skull strip removes brain except brainstem, and then has retesselation error

2013-07-06 Thread Bruce Fischl
Hi Salil have you checked the talairach.xfm to make sure it's accurate? There are options to recon-all to strip less - check out the help. cheers Bruce On Fri, 5 Jul 2013, Salil Soman wrote: > Hi, > I have a study for which the original T1 looks good, was obtained > identically to dozens of ot