if you want to mask the thickness, then use mri_mask

On 10/10/2018 10:30 AM, N Saf wrote:
>
>         External Email - Use Caution
>
> 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 <mailto: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>
>     <mailto: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
>     >     >
>     >     >
>     >     > _______________________________________________
>     >     > Freesurfer mailing list
>     >     > Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     >     <mailto:Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     >     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     >
>     >     _______________________________________________
>     >     Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     <mailto:Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>     >
>     >
>     >     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.
>     >
>     >
>     >
>     > _______________________________________________
>     > Freesurfer mailing list
>     > Freesurfer@nmr.mgh.harvard.edu
>     <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>     _______________________________________________
>     Freesurfer mailing list
>     Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
>     https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer