Hi Bruce, I had Matlab and freesurfer on separate machines. But for now I managed to have Matlab on both, so I can run it. It really helped, thanks! Adiel
2017-07-24 22:33 GMT+03:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
HI Adiel
we distribute all our matlab scripts as part of FreeSurfer
cheers Bruce On Mon, 24 Jul 2017, עדיאל חרבש wrote:
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 fischl@nmr.mgh.harvard.edu: 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 <fischl@nmr.mgh.harvard.edu>: 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 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.
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