mri_info --res file.mgz is probably better than mri_convert
On 7/16/19 11:43 AM, Iglesias Gonzalez, Eugenio wrote:
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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)
*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
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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 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> *MailScanner has detected a possible fraud attempt from "eur01.safelinks.protection.outlook.com" claiming to be* 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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