19 Jul
2016
19 Jul
'16
4:04 p.m.
sorry, perhaps someone else can help you with this. I haven't used plotmesh.
cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote:
Perfect. now if I wanted to use plotmesh with this, what would the variables be for x and y: plotmesh('x,y')
On Tue, Jul 19, 2016 at 11:40 AM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
[aseg,M,mr] = load_mgh('aseg.mgz'); ind = find(aseg == 16); that will give you the indices in the aseg volume of the voxels that have the brainstem label (16). Then you can do what you want with it. The label came from $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: So say I load aseg.mgz into matlab and I want to extract the brainstem in matlab to plot its own volumetric mesh vs. the entire brain, how would I extract the brainstem in matlab? On Tue, Jul 19, 2016 at 11:00 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: but why not just load the aseg.mgz or whatever volume you are using directly into matlab? Then each structure has a different index that you can extract with the find command cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: I attached the page in the last message, maybe it didn't show. I guess they aren't called segmentations, but isolation. https://surfer.nmr.mgh.harvard.edu/fswiki/FreeviewGuide/Freeview WorkingWithData/FreeviewAnatomicalVolumes This link describes the process that am I am working with, and there is an option to save these isolated pieces, and they save as a .vtk file, I am not converting anything Abbie On Tue, Jul 19, 2016 at 10:51 AM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: Hi Abbie I'm not sure what page you mean. The segmentations start life as an .mgz file, so why convert them at all? Just load the aseg.mgz (or whichever segmentation you are interested in) into matlab directly cheers Bruce On Tue, 19 Jul 2016, Abbie McNulty wrote: Hi Bruce, So when I'm at this page, I am separating the different parts of the brain so that in the 3D view they show up as their own entity, and I am trying to individually save them. When I press the save button shown on the left hand side of the screen, it saves as a .vtk file, which makes it difficult to upload into matlab. Is there a way to convert this 3D brain piece as an .mgz file? Thanks On Mon, Jul 18, 2016 at 5:40 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu> wrote: What segmentation do you mean? Where are you getting vtk files? We write the segmentation into .mgz volumes such as aseg.mgz Cheers Bruce On Jul 18, 2016, at 1:19 PM, Abbie McNulty <amcnult1@stanford.edu> wrote: So we were able to figure out how to segment the different parts of the brain using the bert sample, but have run into another problem. I would like to save each segmentation so that I can import it into matlab and create a matrix in order to create a mesh. The volume segment saves a as a .vtk file, which I don't know how to read into matlab. How can I save it as or convert it to a .mgz file so that I can import it into matlab? Thanks! _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. -- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field
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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.
-- Abigail C. McNulty Stanford University Class of 2018 B.A. Candidate in Bioengineering Stanford Women's XC/ Track and Field