Hi Douglas, Thank you, works perfectly. But, I need to know first which structures id's are inside each file. I preferred to extract all the brain map with Matlab, as Bruce commented.
Now I try to match the coordinates, according to the linked you posted. The brain space in results is of 256x256x256 voxels. What are the dimensions of each voxel here? If I need to compare that results to another analysis that come from SPM, so case #2 is the way? And then, I'll need in fact the coordinates from mri_cor2label? Thanks for the fast and useful replies. Adiel 2017-07-24 22:11 GMT+03:00 Douglas Greve <[email protected]>: > If you want all the coordinates for a given segment (eg, left hippo), then > you can run mri_cor2label --i aparc+aseg.mgz --id 17 --l file.label > > 17 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt > > The coordinates will be in "tkregister space" which you can convert to > MNI305 using the info from here: > > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > > using case #2 > > On 7/24/17 2:11 AM, 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 > [email protected]https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > > _______________________________________________ > 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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