Re: [Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

[Douglas N Greve]

Hi Mehul,

Mehul Sampat wrote:
> Thanks Doug.
>
> Using mri_label2vol is a good idea and I will use this approach.
> Now to create the individual binary masks I just need to use 
> mri_label2vol, followed by mri_binarize:
>
> For example:
>
> a. mri_label2vol --seg aparc+aseg.mgz --regheader rawavg.mgz --o 
> aparc+aseg-in-rawavg.mgz --temp aparc+aseg.mgz
The template here should be rawavg.mgz, I think.
> b. mri_binarize --i aparc+aseg-in-rawavg.mgz --match 1022 --o 
> lh-postcentral.nii
>
> Also, when I looked at the help, I first thought I could do the same 
> thing with mri_annotation2label followed by mri_label2vol .
>
> for example:
>
> a. mri_annotation2label --subject bert --hemi lh --annotation aparc 
> --outdir labels
> b. mri_label2vol --label ../labels/lh.postcentral.label --regheader 
> rawavg.mgz --o lh-postcentral.nii --temp aparc+aseg.mgz
Again, use rawavg.mgz as the temp. Also you should be able to use 
mri_label2vol directly on the annotation (with --annot).

doug
>
> But when I checks the results, (from using  mri_annotation2label 
> followed by mri_label2vol), the individual binary mask looks incorrect
> Did I make an error in the second approach ?
>
> Thanks
> Mehul
>
>
>
>
> On Tue, Jul 13, 2010 at 2:41 PM, Douglas N Greve 
> mailto:gr...@nmr.mgh.harvard.edu>> wrote:
>
> I think either should work, though I am more comfortable with
> mri_vol2vol. Depending on what you are doing you might want to use
> mri_label2vol. This can convert the aseg.mgz directly to the
> native anatomical space. The main difference is that it will
> resolve boundary voxels by voting. With your method, you will have
> some voxels that  will be in more than one label, which may or may
> not be a problem depending on what you are doing.
>
> doug
>
> Mehul Sampat wrote:
>
> Hi Folks,
>
> I would like to create binary masks for any given structure in
> aseg.mgz and aparc+aseg.mgz.
> I would then also like to map the masks back to native space.
>
> I think, I should use mri_binarize followed by mri_convert as
> shown in the two examples below:
>
> Example 1:
> a. mri_binarize --i mri/aseg.mgz --match 10 --o
> deep-gm-rois/lh-thalamus.mgz
> b. mri_convert -rl mri/orig/001.mgz -rt nearest
> deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii
>
> Example 2:
> a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o
> ctx-gm-rois/lh-postcentral.mgz
> b. mri_convert -rl mri/orig/001.mgz -rt nearest
> ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii
>
> Ques 1: Is the best approach for this task ?
>
> I noticed in the FAQ that mri_vol2vol is recommended for
> conversion from freesurfer space to anantomical space.
>
> Ques 2: Is it better to use mri_vol2vol than mri_convert with
> the reslice option ?
> Thanks
> Mehul
>
> 
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> 
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> -- 
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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
> 
>
>

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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

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Re: [Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

[Mehul Sampat]

Thanks Doug.

Using mri_label2vol is a good idea and I will use this approach.
Now to create the individual binary masks I just need to use mri_label2vol,
followed by mri_binarize:

For example:

a. mri_label2vol --seg aparc+aseg.mgz --regheader rawavg.mgz --o
aparc+aseg-in-rawavg.mgz --temp aparc+aseg.mgz
b. mri_binarize --i aparc+aseg-in-rawavg.mgz --match 1022 --o
lh-postcentral.nii

Also, when I looked at the help, I first thought I could do the same thing
with mri_annotation2label followed by mri_label2vol .

for example:

a. mri_annotation2label --subject bert --hemi lh --annotation aparc --outdir
labels
b. mri_label2vol --label ../labels/lh.postcentral.label --regheader
rawavg.mgz --o lh-postcentral.nii --temp aparc+aseg.mgz

But when I checks the results, (from using  mri_annotation2label followed by
mri_label2vol), the individual binary mask looks incorrect
Did I make an error in the second approach ?

Thanks
Mehul




On Tue, Jul 13, 2010 at 2:41 PM, Douglas N Greve
wrote:

> I think either should work, though I am more comfortable with mri_vol2vol.
> Depending on what you are doing you might want to use mri_label2vol. This
> can convert the aseg.mgz directly to the native anatomical space. The main
> difference is that it will resolve boundary voxels by voting. With your
> method, you will have some voxels that  will be in more than one label,
> which may or may not be a problem depending on what you are doing.
>
> doug
>
> Mehul Sampat wrote:
>
>> Hi Folks,
>>
>> I would like to create binary masks for any given structure in aseg.mgz
>> and aparc+aseg.mgz.
>> I would then also like to map the masks back to native space.
>>
>> I think, I should use mri_binarize followed by mri_convert as shown in the
>> two examples below:
>>
>> Example 1:
>> a. mri_binarize --i mri/aseg.mgz --match 10 --o
>> deep-gm-rois/lh-thalamus.mgz
>> b. mri_convert -rl mri/orig/001.mgz -rt nearest
>> deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii
>>
>> Example 2:
>> a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o
>> ctx-gm-rois/lh-postcentral.mgz
>> b. mri_convert -rl mri/orig/001.mgz -rt nearest
>> ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii
>>
>> Ques 1: Is the best approach for this task ?
>>
>> I noticed in the FAQ that mri_vol2vol is recommended for conversion from
>> freesurfer space to anantomical space.
>>
>> Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice
>> option ?
>> Thanks
>> Mehul
>>
>> 
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>>
>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@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
>
>
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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.

Re: [Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

[Douglas N Greve]

I think either should work, though I am more comfortable with 
mri_vol2vol. Depending on what you are doing you might want to use 
mri_label2vol. This can convert the aseg.mgz directly to the native 
anatomical space. The main difference is that it will resolve boundary 
voxels by voting. With your method, you will have some voxels that  will 
be in more than one label, which may or may not be a problem depending 
on what you are doing.

doug

Mehul Sampat wrote:
> Hi Folks,
>
> I would like to create binary masks for any given structure in 
> aseg.mgz and aparc+aseg.mgz.
> I would then also like to map the masks back to native space.
>
> I think, I should use mri_binarize followed by mri_convert as shown in 
> the two examples below:
>
> Example 1:
> a. mri_binarize --i mri/aseg.mgz --match 10 --o 
> deep-gm-rois/lh-thalamus.mgz
> b. mri_convert -rl mri/orig/001.mgz -rt nearest 
> deep-gm-rois/lh-thalamus.mgz deep-gm-rois/lh-thalamus.nii
>
> Example 2:
> a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o 
> ctx-gm-rois/lh-postcentral.mgz
> b. mri_convert -rl mri/orig/001.mgz -rt nearest 
> ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii
>
> Ques 1: Is the best approach for this task ?
>
> I noticed in the FAQ that mri_vol2vol is recommended for conversion 
> from freesurfer space to anantomical space.
>
> Ques 2: Is it better to use mri_vol2vol than mri_convert with the 
> reslice option ?
> Thanks
> Mehul
>
> 
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

-- 
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@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

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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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but does not contain patient information, please contact the sender and properly
dispose of the e-mail.

[Freesurfer] creating binary masks for any given structure in aseg.mgz or aparc+aseg.mgz

[Mehul Sampat]

Hi Folks,

I would like to create binary masks for any given structure in aseg.mgz and
aparc+aseg.mgz.
I would then also like to map the masks back to native space.

I think, I should use mri_binarize followed by mri_convert as shown in the
two examples below:

Example 1:
a. mri_binarize --i mri/aseg.mgz --match 10 --o deep-gm-rois/lh-thalamus.mgz
b. mri_convert -rl mri/orig/001.mgz -rt nearest deep-gm-rois/lh-thalamus.mgz
deep-gm-rois/lh-thalamus.nii

Example 2:
a. mri_binarize --i mri/aparc+aseg.mgz --match 1022 --o
ctx-gm-rois/lh-postcentral.mgz
b. mri_convert -rl mri/orig/001.mgz -rt nearest
ctx-gm-rois/lh-postcentral.mgz ctx-gm-rois/lh-postcentral.nii

Ques 1: Is the best approach for this task ?

I noticed in the FAQ that mri_vol2vol is recommended for conversion from
freesurfer space to anantomical space.

Ques 2: Is it better to use mri_vol2vol than mri_convert with the reslice
option ?
Thanks
Mehul
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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.