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Dear Douglos,

as you recommended, I used the --outmask and create the binary mask of a label in mgh format. as I use the mri_binarize command with this mask and ?h.thickness; the output is binary too or if I use --match flag or --min --max flag the out put is 1 for those range, but I want the thickness values on my mask, not 1 all over it , how should I do that?

any detail information will be appreciated.

BRG,
Nazanin
 

On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D. <DGREVE@mgh.harvard.edu> wrote:
Use the --outmask option

On 10/07/2018 08:59 AM, N Saf wrote:
>
>         External Email - Use Caution
>
> Dear Douglos,
>
> I did not understand how to use mri_label2label with the mask
> option(there is srcmask options not mask alone !). I extract my labels
> and as you explained I wanted to create i.e. binary mask of
> rh.fusiform.label  with mri_label2label :
>   mri_label2label  --srcsubject case1 --srclabel rh.fusiform.label
> --trgsubject case1 --trglabel outputlabel.mgh --regmethod surface
> --hemi rh
>
> but it creats another label file not binary with mgh format I did not
> get how can I create mybinary.mgh mask in order to use in third
> command "mri_binarize --i lh.thickness --mask youmask.mgh --o
> lh.thickness.masked.mgh"
>
> would you please help me with this, it would be a great favor.
>
> Best regards,
> Nazanin
>
> On Mon, Jul 30, 2018 at 10:59 PM Douglas N. Greve
> <dgreve@mgh.harvard.edu <mailto:dgreve@mgh.harvard.edu>> wrote:
>
>     Yes, that should work. You can create a mask by breaking the
>     annotation
>     into labels (mri_annotation2label), then converting the label into a
>     binary mask (mri_label2label with --mask option), then
>     mri_binarize --i
>     lh.thickness --mask youmask.mgh --o lh.thickness.masked.mgh
>
>
>     On 07/30/2018 01:47 AM, N Saf wrote:
>     >
>     >         External Email - Use Caution
>     >
>     > Dear Freesurfer Experts,
>     >
>     > I wonder how can I show the cortical thickness surface on just one
>     > region of my interest in Freeview.  assume that I want to see the
>     > thickness surface of one of the regions in DKTatlas. does it
>     work if I
>     > make a binary mask of that specific region on
>     aparcDKTatlas.annot and
>     > then multiply it to the ?h.thickness surface ?? any help will be
>     > appreciated.
>     >
>     > Best Regards,
>     > Nazanin
>     >
>     >
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