Re: [Freesurfer] masking cortical thickness

[N Saf]

External Email - Use Caution

Hi,

Thank you so much , it works.

BRG,
Nazanin

On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. <
dgr...@mgh.harvard.edu> wrote:

> 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.
> > mailto:dgr...@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
> > > mailto:dgr...@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
> > 
> > >  > >
> > > > 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
> > >
> > >
> > > 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.
> > >
> > >
> > >
> > > ___
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> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> >

Re: [Freesurfer] masking cortical thickness

[Greve, Douglas N.,Ph.D.]

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. 
> mailto:dgr...@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
> > mailto:dgr...@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
> 
> >      >
> >     > 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
> >
> >
> >     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
> 
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] masking cortical thickness

[N Saf]

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. <
dgr...@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
> > mailto:dgr...@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
> > 
> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
> >
> > ___
> > Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu  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
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
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Re: [Freesurfer] masking cortical thickness

[Greve, Douglas N.,Ph.D.]

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 
> mailto:dgr...@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
> 
> > 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
>
>
> 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.
>
>
>
> ___
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Re: [Freesurfer] masking cortical thickness

[N Saf]

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 
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
> > 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
>
>
> 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.
>
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Re: [Freesurfer] masking cortical thickness

[Douglas N. Greve]

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
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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contains patient information, please contact the Partners Compliance HelpLine at
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but does not contain patient information, please contact the sender and properly
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[Freesurfer] masking cortical thickness

[N Saf]

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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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
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but does not contain patient information, please contact the sender and properly
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Re: [Freesurfer] Masking cortical thickness

[Bruce Fischl]

I think you could just load the cortex.label map onto the surface and 
edit those regions out. Then they will not contribute to smoothed maps, 
etc...  Doug: any reason this wouldn't work?

Bruce

On Tue, 13 Feb 2018, James Hobart wrote:

> Hi all,
> I am looking to mask out a small region of the GM when calculating the 
> cortical thickness of ROIs
> across the brain. Essentially I have a couple of cases with small GM lesions 
> where the cortical
> thickness is less likely to be meaningful for my analysis.
> 
> I have binary lesion masks and also full recon-all s for these cases. I was 
> thinking I would need to
> mask the cortical thickness map somehow (potentially mapping the mask volume 
> to a surface?) before
> using the mris_anatomical_stats to calculate cortical thickness.
> 
> Is this the best way to go about this?
> 
> Many thanks
> James
> 
>
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[Freesurfer] Masking cortical thickness

[James Hobart]

Hi all,

I am looking to mask out a small region of the GM when calculating the
cortical thickness of ROIs across the brain. Essentially I have a couple of
cases with small GM lesions where the cortical thickness is less likely to
be meaningful for my analysis.

I have binary lesion masks and also full recon-all s for these cases. I was
thinking I would need to mask the cortical thickness map somehow
(potentially mapping the mask volume to a surface?) before using the
mris_anatomical_stats to calculate cortical thickness.

Is this the best way to go about this?

Many thanks
James
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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
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dispose of the e-mail.