This is actually a problem with mri_label2vol. I have fixed it and put a 
new copy here
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_label2vol
run it like this

mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o 
sc.nii --tkr-template orig.mgz

On 12/3/19 8:23 AM, ZORO wrote:
>
>         External Email - Use Caution
>
> Hi Douglas,
> Thanks for your reply!
> I tried, but the volume and T1 still don't align.
>
> my purpose:
> make a mask of superior colliculus
>
> Here is how I did:
> 1) tkregister2 --mov T1.nii --s sub01 --regheader --noedit --reg 
> register.dat
> 2) open freeview and load orig.mgz→ New ROI and select orig.mgz as the 
> template volume→ draw ROI of superior colliculus slice by slice and 
> save it as sc.label
> 3) mri_label2vol --label sc.label --temp T1.nii --reg register.dat --o 
> sc.nii --invertmtx
>
> The problem:
> sc.nii and T1.nii don't align, the ROI of superior colliculus are in 
> the wrong place.
>
> I would highly appreciate If you have any suggestions as the ways to 
> get superior colliculus' ROI or mask.
>
>
>
> At 2019-12-03 00:02:15, "Greve, Douglas N.,Ph.D." 
> <dgr...@mgh.harvard.edu> wrote:
>
>     Try adding  --invertmtx to the mri_label2vol command
>
>     On 11/28/2019 4:35 AM, Zoro wrote:
>>
>>             External Email - Use Caution
>>
>>     Thanks for your reply and sorry to bother you again. The problem
>>     is that the volume converted from label which drew by freeview
>>     does not match T1.
>>
>>     Happy Thanksgiving day!
>>
>>     *发件人**: *Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>
>>     *发送时间**: *2019年11月28日0:59
>>     *收件人**: *freesurfer@nmr.mgh.harvard.edu
>>     <mailto:freesurfer@nmr.mgh.harvard.edu>
>>     *主题**: *Re: [Freesurfer] Converting labels drew by freeview to
>>     volumeError: coordinate mismatch
>>
>>     I'm not sure what the problem is. You say that they match when
>>     you load the T1 and the sc. If so, what is the problem?
>>
>>     On 11/27/2019 7:57 AM, zorothustra wrote:
>>
>>         *        External Email - Use Caution *
>>
>>         Hello Freesurfer Developers,
>>
>>         I'm trying to get superior colliculus' ROI mannually by
>>         freeview. I load "orig.mgz" as volumes and set the "orig.mgz"
>>         as the ROI's template then draw the ROI and save it as a
>>         label file. After that I use "mri_label2vol --label sc.label
>>         --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my
>>         initial structure image, "register.dat" got from the code:"
>>         tkregister2 --mov T1.nii --s SUB --regheader --noedit --reg
>>         register.dat", and it worked, but the coordinate mismatch,
>>         much different from the SC's position in the T1 space( Load
>>         T1.nii as volume and SC.label as ROI in freeview, and they
>>         are matched).
>>
>>         Can anyone help me? Thank you!
>>
>>         1)FreeSurfer version: freesurfer-local-build-dev-20191104
>>
>>         2)platform: Ubuntu 18.04
>>
>>
>>
>>
>>
>>
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>
>
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