Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

2016-09-05 Thread Ruyuan Zhang
Not sure it's helpful. The simplest way I can think of is to directly edit WM.mgz. You can load wm.mgz into matlab, it's basically a 3D matrix. You can directly set values for wm matrix, for instance wm(wm(:)>200)=110; Then you save the new wm matrix into wm.mgz. On 9/5/16 10:54 AM,

Re: [Freesurfer] Coordinates of particular volumes

2016-09-04 Thread Ruyuan Zhang
Hi, Aziz You can use MRIread function to read in a volume (i.e. brainmask.mgz). You will get a structure, which contains a field called ras2vox. cheers ruyuan On 9/4/16 6:23 PM, Aziz Nanthaamornphong wrote: Hi, For example, I want to know the list of x, y, z coordinates of a left