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-boun...@nmr.mgh.harvard.edu> on behalf of Min > Zhang <jacqueline.m.zh...@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.igles...@ucl.ac.uk <mailto:e.igles...@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-boun...@nmr.mgh.harvard.edu > <mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Min > Zhang <jacqueline.m.zh...@gmail.com > <mailto:jacqueline.m.zh...@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> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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