26 Jul
2017
26 Jul
'17
2:13 p.m.
finding coordinates is the same problem as putting the results into the same space (except probably harder). There is not a simple formula for converting one to the other. Eg, fsaverage uses MNI305 space. What is SPM using? You have to figure out all these things to convert
On 07/26/2017 04:10 AM, עדיאל חרבש wrote:
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 <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
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 <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > 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> > <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 >> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto: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 <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <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> >> <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 >> Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> <mailto:Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > <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> > <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 > Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 <https://gate.nmr.mgh.harvard.edu/filedrop2> www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer <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
--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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/