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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/BrainstemSubstructureshttps://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.comhttps://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
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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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferhttps://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