Hi Bruce, It may really help to shorten and ease the procedure, thanks. I see that I should clone all your matlab repository to use this function?
I will look over mri_extract_labels as well. Best, Adiel 2017-07-24 17:02 GMT+03:00 Bruce Fischl <[email protected]>: > Hi Adiel > > in matlab you could do something like: > > cd $SUBJECTS_DIR/<subject id>/mri > matlab > >> [v,M,mr] = load_mgh('aseg.mgz'); >>> left_hippo_indices = find(v == 17); >>> >> > > where the '17' comes from $FREESURFER_HOME/FreeSurferColorLUT.txt and is > the index for left hippocampus. > > Is that would you mean? Or you could use mri_extract_labels to build > volumes that have only the labels you want in them. > > cheers > Bruce > > > > > > On Mon, 24 Jul 2017, עדיאל חרבש wrote: > > Hi Bruce, >> Thanks for the reply. >> By "coordinates" I mean all the voxels that belong to a certain >> structure. I >> think it's called "labels"? I interest in the main structures like >> Hippocampus, Thalamus, Cerebellum, Amygdala, corpus callosum, etc. If the >> standard segmentation segments in that specificity only the lobes, it can >> be >> good enough... >> I see the .mgz files, but can not extract them... How should I do that? >> >> Thank for the patience.. >> Adiel >> >> >> 2017-07-23 18:09 GMT+03:00 Bruce Fischl <[email protected]>: >> Hi Adiel >> >> what kind of coordinates do you mean, and which brain structures >> are you interested in? Our standard segmentation is sampled into >> the volume in files named aparc*+aseg.mgz, but the Brodmann area >> estimates are on the surface. >> >> cheers >> Bruce >> >> >> On Sun, 23 Jul 2017, עדיאל חרבש wrote: >> >> Hi, >> I'm very new to Freesurfer, and actually work with >> some exist results of >> other people. The results are from the call of >> "-recon all -autorun". >> I try to get all the coordinates of each of the >> structures of the brain, >> that segmented. I can find on files only the volumes >> of some structures and >> something that look like detailed coordinates of >> Brodman Areas only. But I >> can't find the detailed coordinates of all >> structures in brain. >> >> I'll be grateful if someone can guide me where can I >> find it, or what should >> I do to get these results. >> >> Thanks, >> Adiel >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> [email protected] >> 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. >> >> >> >> > _______________________________________________ > Freesurfer mailing list > [email protected] > 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. > >
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