Hi Doug,
Thanks for your reply. So the template file is merely used for its size and geometry to fit the output, right?
By the way, could you tell me the difference between rawavg.mgz and orig.mgz? Suppose I have just 1 scan, they are the same, and if I have two or more scans, rawavg is the average and orig is always the first scan?
Sorry for some simple questions.
Thanks, Daniel
On Jul 17, 2013, at 12:18 PM, "Douglas N Greve" greve@nmr.mgh.harvard.edu wrote:
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 12:11 PM, Yang, Daniel wrote:
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 "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
On 7/16/13 9:13 PM, "Douglas Greve" <greve@nmr.mgh.harvard.edu mailto:greve@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 DK atlas, and I know that I can use tkregister2 to obtain a register.dat, and then mri_annotation2label + mri_label2vol to convert the annotation of the ROI to an .nii.gz.
However, it seems that the end product is in the TAL space? If yes, how can I convert it to the MNI 152 space?
Many thanks!!
Best, Daniel -- Yung-Jui "Daniel" Yang, PhD Postdoctoral Researcher Yale Child Study Center New Haven, CT (203) 737-5454
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