Oh, sure you are right. But each analysis is done on different protocols, and also, for now I already have many of analysis results that has been run on the SPM and on Freesurfer, and has a difference in coordinates. So- for now, what is the right way to treat that? the link that you gave up here? And for future- how can I set the dimensions for the results in freesurfer? For example, my data is 432x432x150, but the segmentation results are 256x256x256.
Thank you. Adiel 2017-07-25 20:51 GMT+03:00 Douglas N Greve <[email protected]>: > I would put the spm and fs analysis into the same space > > > On 07/25/2017 10:19 AM, עדיאל חרבש wrote: > > 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] > > <mailto:[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 > > <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] <mailto:[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] > >> <mailto:[email protected]> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <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 > >> <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] > >> <mailto:[email protected]> > >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > > > > > > _______________________________________________ > > Freesurfer mailing list > > [email protected] <mailto:[email protected]. > harvard.edu> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > <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 > > <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 > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > [email protected] > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 > www.nmr.mgh.harvard.edu/facility/filedrop/index.html > Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ > > _______________________________________________ > Freesurfer mailing list > [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.
