[Freesurfer] new rawavg in fs5 and reprocessing

2010-09-07 Thread k . b . walhovd
Hi, I see there's a new motion correction procedure in fs5, meaning that the rawavg is created differently. When reprocessing data, should we then do everything over, including remaking the rawavg and all edits? I'm asking esp. w/ regards to edits - can they possibly be slightly wrong if kept? An

Re: [Freesurfer] Talairach_avi and eTIV, version 3.0.5 vs 4.0.5

2008-06-23 Thread k . b . walhovd
Hi yes, the FS ICVs mostly seem to work :-) I still think one should watch out for outliers. We had a sample of 28 kids aged 8-13 yrs, and the ICVs were quite a bit off and useless for two of those, so I would check all carefully especially if you have a group that may have smaller than normal ad

Re: [Freesurfer] what is the prerequisite of cc in cortparc?

2008-01-23 Thread k . b . walhovd
Thanks, I'll try that. Will I then need to redo all steps fromm -ccseg onwards if I want a correct wmparc at the end, or can I safely skip some? For instance, I could do -ccseg -cortribbon -cortparc -aparc2aseg -wmparc? Best, Kristine > Kristine, > You should be able to use -ccseg which occurs a

Re: [Freesurfer] what is the prerequisite of cc in cortparc?

2008-01-22 Thread k . b . walhovd
Thanks! The MRI_cc works fine. It's just that I want to use the entire wmparc, and I worry that it may be skewed when the cc is not in there. The cingulate parcellations look a little off. Do you think there's any step in -autorecon2 (before -cortribbon) after the aseg I might try to start reproce