Re: [Freesurfer] Bad design matrix

2015-03-01 Thread Douglas Greve
Try demeaning your covariates. By demeaning, I mean to compute the mean across all subjects, then subtract the mean from all values (for each covariate). doug On 3/1/15 2:40 AM, Anders Hougaard wrote: Dear all, I'm comparing cortical thickness of a group of patients to a group of

Re: [Freesurfer] Projection of CBF maps on fsaverage and smooth

2015-03-01 Thread Douglas Greve
Basically looks ok. The only things that jump out at me are that you are using regheader (I would create a registration file with bbregister rather than assuming that there was no motion between the anatomical and the ASL). Where did brain.fsaverage.lh.mgh come from? doug On 2/27/15 2:16

Re: [Freesurfer] regional surface area differences

2015-03-01 Thread Douglas Greve
On 2/27/15 3:41 PM, aqure...@nmr.mgh.harvard.edu wrote: Hi Freesurfer group, I wanted to use mris_preproc to calculate regional differences in surface area between two groups. Ideally I would like to use something that is vertex-wise and preserves regional area, but I've had trouble with

Re: [Freesurfer] freeview registration

2015-03-01 Thread Douglas Greve
I think that freeview does not correctly generate the registration file. You can use it to check the regsitration, but us tkregister if you need to edit it. doug On 2/27/15 10:18 AM, Xiaomin Yue wrote: Hi All, After using freeview to manually adjust the registration between a