Re: [Freesurfer] convert surface label on to functional image

The easiest thing is to use mri_label2vol, something like mri_label2vol --label yourlabel.label --temp functemplate.nii --reg register.dat --proj frac 0 1 .1 --hemi lh --subject subject --o yourlabel.nii

doug

Zhangyuanchao wrote:

Thanks for your response!

In fact, the label that I want to convert to functional space was obtained by between-group comparisons, so it does not belong to any existing parcellation template.

What should I do in this case?

Thanks!

Best,

--- *11年12月13日，周二, Douglas N Greve /greve@nmr.mgh.harvard.edu/* 写道：

发件人: Douglas N Greve <greve@nmr.mgh.harvard.edu>
主题: Re: [Freesurfer] convert surface label on to functional image
收件人: "Zhangyuanchao" <woshizhangyc@yahoo.cn>
抄送: freesurfer@nmr.mgh.harvard.edu
日期: 2011年12月13日,周二,上午5:48

Hi Yuanchao, I would recommend that you use the aparc+aseg.mgz
file for this. This file has cortical labels already in the
volume, you just need to map them to your functional space,
something like

mri_label2vol --aparc+aseg --temp functemplate.nii --reg
register.dat --o aparc+aseg.fmri.nii

doug

Zhangyuanchao wrote:
> hi, expert,
>
> By mapping a surface label to a functional template, I want to
extract the corresponding cortical gray matter region in the
functional space. I know I should use the mri_label2vol command.
> In the help page of mri_label2vol, I see some examples of this
command.
>
> 2. Convert a surface label into a binary mask in the functional
space.
> Fill in all the cortical gray matter. Require that a functional
voxel
> be filled at least 30% by the label:
>
> mri_label2vol   --label lh-avg_central_sulcus.label   --temp
f.nii   --reg register.dat   --fillthresh .3   --proj frac 0 1
.1   --subject bert --hemi lh
>   --o cent-lh.nii
>
> 3. Convert a surface label into a binary mask in the functional
space.
> Sample a 1mm ribbon 2mm below the gray/white surface. Do not
require a fill threshold:
>
> mri_label2vol   --label lh-avg_central_sulcus.label   --temp
f.nii   --reg register.dat   --proj abs -3 -2 .1   --subject bert
--hemi lh
>   --o cent-lh.nii
>
> I want to extract the cortical gray matter on the functional
images corresponding to the surface label. I do not know which of
the above commands could obtain the result I want and which
parameters I should use to obtain what I want.
>
> For example 3, I do not quite catch what "Sample a 1mm ribbon
2mm below the gray/white surface. " this sentence means.
> Thanks for your help!
>
>
> Best
>
> Yuanchao
>
>
------------------------------------------------------------------------
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
</mc/compose?to=Freesurfer@nmr.mgh.harvard.edu>
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu </mc/compose?to=greve@nmr.mgh.harvard.edu>
Phone Number: 617-724-2358 Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html



The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.