Hi, all. I want to convert a freesufer label to diffusion mask with the following approach.
# tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat
# mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation aparc.a2009s tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat
# mri_label2vol --label ./labels/rh.entorhinal.label --temp S0001_FA.nii.gz --subject S0001 --hemi rh --o rh.entorhinal.nii.gz --proj frac 0 1 .1 --fillthresh 0.3 --reg register.dat
I wonder whether this is correct? In particular, what I am not sure about is the generation about the register.mat in the first line cmd.
Best, Xiang-zhen
【小孔成像】http://www.conxz.net
Usually, the register.dat is generated with bbregister. What you have may work if the DTI was acquired in the same session as the anatomical and the subject did not move between the two. doug
On 09/11/2014 08:16 AM, Xiang-zhen Kong wrote:
Hi, all. I want to convert a freesufer label to diffusion mask with the following approach. # tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation aparc.a2009s tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_label2vol --label ./labels/rh.entorhinal.label --temp S0001_FA.nii.gz --subject S0001 --hemi rh --o rh.entorhinal.nii.gz --proj frac 0 1 .1 --fillthresh 0.3 --reg register.dat I wonder whether this is correct? In particular, what I am not sure about is the generation about the *register.mat* in the first line cmd. Best, Xiang-zhen
【小孔成像】http://www.conxz.net
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks very much, Douglas. This is very helpful.
Best, Xiang-zhen
【小孔成像】http://www.conxz.net
From: Douglas N Greve Date: 2014-09-11 22:48 To: freesurfer Subject: Re: [Freesurfer] from freesufer label to diffusion mask
Usually, the register.dat is generated with bbregister. What you have may work if the DTI was acquired in the same session as the anatomical and the subject did not move between the two. doug
On 09/11/2014 08:16 AM, Xiang-zhen Kong wrote:
Hi, all. I want to convert a freesufer label to diffusion mask with the following approach. # tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_annotation2label --subject S0001 --hemi rh --outdir ./labels --annotation aparc.a2009s tkregister2 --mov S0001_FA.nii.gz --noedit --s S0001 --regheader --reg register.dat # mri_label2vol --label ./labels/rh.entorhinal.label --temp S0001_FA.nii.gz --subject S0001 --hemi rh --o rh.entorhinal.nii.gz --proj frac 0 1 .1 --fillthresh 0.3 --reg register.dat I wonder whether this is correct? In particular, what I am not sure about is the generation about the *register.mat* in the first line cmd. Best, Xiang-zhen
【小孔成像】http://www.conxz.net
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Douglas N Greve -
Xiang-zhen Kong