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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
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:
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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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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 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 CautionDear 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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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.
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 > > > _______________________________________________ > 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 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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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 CautionDear 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 > > > _______________________________________________ > 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 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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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
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Hi,
Thank you so much , it works.
BRG, Nazanin
On Wed, Oct 10, 2018 at 9:41 PM Greve, Douglas N.,Ph.D. < DGREVE@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 CautionDear 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>
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Greve, Douglas N.,Ph.D.
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N Saf