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Pixel values in Brainstem segmentation

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Min Zhang

16 Jul 2019 16 Jul '19

9:53 a.m.

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I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. Many Thanks!

Best

Jackie

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Min Zhang

16 Jul 16 Jul

9:57 a.m.

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I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. I used the result in *brainstemSsLabels.v10.mgz. *Many Thanks!

Best

Jackie

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Iglesias Gonzalez, Eugenio

11:15 a.m.

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Dear Jackie, You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Also: you can obtain the voxel size with: mri_info brainstemSsLabels.v10.mgz Cheers, /E

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Min Zhang jacqueline.m.zhang@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 16 July 2019 at 09:58 To: "freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation

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To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. I used the result in brainstemSsLabels.v10.mgz. Many Thanks!

Best

Jackie

Reply

Min Zhang

11:27 a.m.

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Hi, Eugenia

I need the real area size of the brainstem in one slice, I can calculate the total pixels in the area from *brainstemSsLabels.v10.mgz*, I need the real pixel size of it, than I can calculate the real area size. Many Thanks!

Best Jackie

On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio < e.iglesias@ucl.ac.uk> wrote:

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Dear Jackie,

You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see:

https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures

Also: you can obtain the voxel size with:

mri_info brainstemSsLabels.v10.mgz

Cheers,

/E

--

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Min Zhang < jacqueline.m.zhang@gmail.com> *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, 16 July 2019 at 09:58 *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Pixel values in Brainstem segmentation
   External Email - Use Caution        *
To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. I used the result in *brainstemSsLabels.v10.mgz. *Many Thanks!

Best

Jackie

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

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Iglesias Gonzalez, Eugenio

11:43 a.m.

New subject: Pixel values in Brainstem segmentation {Disarmed}

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Hi again, mri_convert will give you the voxel size, which is isotropic. Multiply 2 of the dimensions and you’ve got the area. Also: rather than counting pixels from the discrete segmentation, I highly recommend that you produce soft segmentations as explained in my previous email. Then, you can weigh the area of each pixel in each slice by it’s probability. Cheers, /Eugenio

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com

From: freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Min Zhang jacqueline.m.zhang@gmail.com Reply-To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Date: Tuesday, 16 July 2019 at 11:28 To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution Hi, Eugenia

I need the real area size of the brainstem in one slice, I can calculate the total pixels in the area from brainstemSsLabels.v10.mgz, I need the real pixel size of it, than I can calculate the real area size. Many Thanks!

Best Jackie

On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.ukmailto:e.iglesias@ucl.ac.uk> wrote:

External Email - Use Caution Dear Jackie, You may want to use the soft segmentations; you can obtain them by setting the environment variable WRITE_POSTERIORS to 1 before running the code, see: https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures&data=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291022044&sdata=VfgJV4O%2F3mbmdk3baaSZyXVAIM0p2AfY8WSqaLvZ%2B20%3D&reserved=0 Also: you can obtain the voxel size with: mri_info brainstemSsLabels.v10.mgz Cheers, /E

-- Juan Eugenio Iglesias Senior research fellow CMIC (UCL), MGH (HMS) and CSAIL (MIT) http://www.jeiglesias.com https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com&data=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291032039&sdata=uGg%2BWF942tA6GrHgPtWV1psavUg%2FBn%2F9RtDywLNJcuQ%3D&reserved=0

From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Min Zhang <jacqueline.m.zhang@gmail.commailto:jacqueline.m.zhang@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Tuesday, 16 July 2019 at 09:58 To: "freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu" <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Pixel values in Brainstem segmentation

External Email - Use Caution

To whom it may concern

I used the freesufer brainstem segmentation, and I want to calculate the area of the segmented brainstem by slices. Would you like to let me know the pixel value of all three directions. I used the result in brainstemSsLabels.v10.mgz. Many Thanks!

Best

Jackie _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer&data=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291032039&sdata=zyYCqHaAsTQIuHiRjn6rYWwEo2TtFZsiBs9BtleUYCM%3D&reserved=0

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Greve, Douglas N.,Ph.D.

12:02 p.m.

New subject: Pixel values in Brainstem segmentation {Disarmed}

mri_info --res file.mgz is probably better than mri_convert

On 7/16/19 11:43 AM, Iglesias Gonzalez, Eugenio wrote:

External Email - Use Caution

Hi again,

mri_convert will give you the voxel size, which is isotropic. Multiply 2 of the dimensions and you’ve got the area.

Also: rather than counting pixels from the discrete segmentation, I highly recommend that you produce soft segmentations as explained in my previous email. Then, you can weigh the area of each pixel in each slice by it’s probability.

Cheers,

/Eugenio

--

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

http://www.jeiglesias.com

*From: *freesurfer-bounces@nmr.mgh.harvard.edu on behalf of Min Zhang jacqueline.m.zhang@gmail.com *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Tuesday, 16 July 2019 at 11:28 *To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject: *Re: [Freesurfer] Pixel values in Brainstem segmentation

* External Email - Use Caution *

Hi, Eugenia

I need the real area size of the brainstem in one slice, I can calculate the total pixels in the area from /brainstemSsLabels.v10.mgz/, I need the real pixel size of it, than I can calculate the real area size. Many Thanks!

Best

Jackie

On Tue, Jul 16, 2019 at 11:16 AM Iglesias Gonzalez, Eugenio <e.iglesias@ucl.ac.uk mailto:e.iglesias@ucl.ac.uk> wrote:
*        External Email - Use Caution *

Dear Jackie,

You may want to use the soft segmentations; you can obtain them by
setting the environment variable WRITE_POSTERIORS to 1 before
running the code, see:

*MailScanner has detected a possible fraud attempt from
"eur01.safelinks.protection.outlook.com" claiming to be*
https://surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures
<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FBrainstemSubstructures&data=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291022044&sdata=VfgJV4O%2F3mbmdk3baaSZyXVAIM0p2AfY8WSqaLvZ%2B20%3D&reserved=0>

Also: you can obtain the voxel size with:

mri_info brainstemSsLabels.v10.mgz

Cheers,

/E

-- 

Juan Eugenio Iglesias

Senior research fellow

CMIC (UCL), MGH (HMS) and CSAIL (MIT)

*MailScanner has detected a possible fraud attempt from
"eur01.safelinks.protection.outlook.com" claiming to be*
http://www.jeiglesias.com
<https://eur01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.jeiglesias.com&data=02%7C01%7C%7C57107bbc455449bc08aa08d70a024bb5%7C1faf88fea9984c5b93c9210a11d9a5c2%7C0%7C0%7C636988877291032039&sdata=uGg%2BWF942tA6GrHgPtWV1psavUg%2FBn%2F9RtDywLNJcuQ%3D&reserved=0>


*From: *<freesurfer-bounces@nmr.mgh.harvard.edu
<mailto:freesurfer-bounces@nmr.mgh.harvard.edu>> on behalf of Min
Zhang <jacqueline.m.zhang@gmail.com
<mailto:jacqueline.m.zhang@gmail.com>>
*Reply-To: *Freesurfer support list
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Date: *Tuesday, 16 July 2019 at 09:58
*To: *"freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>"
<freesurfer@nmr.mgh.harvard.edu
<mailto:freesurfer@nmr.mgh.harvard.edu>>
*Subject: *Re: [Freesurfer] Pixel values in Brainstem segmentation

*        External Email - Use Caution *

    To whom it may concern

    I used the freesufer brainstem segmentation, and I want to
    calculate the area of the segmented brainstem by slices. Would
    you like to let me know the pixel value of all three
    directions.  I used the result in /brainstemSsLabels.v10.mgz.
    /Many Thanks!

    Best

    Jackie

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Greve, Douglas N.,Ph.D.
Iglesias Gonzalez, Eugenio
Min Zhang