Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

2013-07-17 Thread Douglas N Greve
does htis answer your question? It is from running mri_label2vol with --help doug --temp tempvolid Template volume. The output volume will have the same size and geometry as the template. Template must have geometry information (ie, direction cosines and voxel sizes). Required. On 07/17/2013 1

Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

2013-07-17 Thread Yang, Daniel
Hi Doug, Can I ask a basic question about mri_label2vol? in mri_label2vol, what should be the input for "--temp"? I understand it's supposed to be the template image. If it's the native space, should it be rawavg.mgz or orig.mgz for that individual? Great thanks! Best, Daniel -- Yung-Jui "Da

Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

2013-07-17 Thread Yang, Daniel
Hi Doug, Thanks very much!! Best, Daniel On Jul 16, 2013, at 9:14 PM, "Douglas Greve" mailto:gr...@nmr.mgh.harvard.edu>> wrote: use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the D

Re: [Freesurfer] convert DK atlas ROI to .nii.gz in MNI space

2013-07-16 Thread Douglas Greve
use $FREESURFER_HOME/average/mni152.register.dat doug On 7/16/13 8:36 PM, Yang, Daniel wrote: Dear FreeSurfer Experts, I am interested in a specific ROI in the DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert