Thanks! It seems to rotate the data, though. It does convert the data back to the original dimensions (256X256X176), ut the dimensions are switched. When I save the vol as nii and open in brainvoyager, the sagittal appears in coronal, etc. I tried switching the 256 dimensions, but it remains rotated (in a different rotation), so somehow the conversion to native space rotates the data. Any suggestions? Aya
__________________________________________________ >From Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent Wed 10/27/2010 3:48 PM To Aya Ben Yakov <aya.benya...@weizmann.ac.il> Cc freesurfer@nmr.mgh.harvard.edu Subject Re: [Freesurfer] subcortical structure coordinates Hi Aya, you can convert the aseg back to the original voxel space with mri_convert. I think the cmdline would be: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz -rl = reslice like -rt = resample type cheers Bruce On Wed, 27 Oct 2010, Aya Ben Yakov wrote: > Hi > I'm sorry for all these questions, but I'm very new to freesurfer, and I still > don't really understand how things work. > Is it necessary to convert to nifti? if I understand correctly, mri.vol should > hold the needed information. In what space is this information > (assuming some processing was done on the original data)? > Can I convert it back to the original data space? or to talairach? > The original data includes only 256X256X176, since there were only 176 slices, > yet in mri.vol there are 256 slices. > In short - how can I convert correctly to the original space and to talairach? > > Thanks for your help! > Aya > > > > > > __________________________________________________ > > From Bruce Fischl <fis...@nmr.mgh.harvard.edu > (mailto:fis...@nmr.mgh.harvard.edu)> > Sent Wed 10/27/2010 2:41 PM > To Ørjan Bergmann <orjan.bergm...@medisin.uio.no > (mailto:orjan.bergm...@medisin.uio.no)> > Cc freesurfer@nmr.mgh.harvard.edu (mailto:freesurfer@nmr.mgh.harvard.edu) > Subject Re: [Freesurfer] subcortical structure coordinates > > > yes, and all the volumes have the same index structure, so you can load > any of them. The aseg.mgz contains the labeled volume, with the label to > structure name conversion in the FreeSurferColorLUT.txt > > cheers > Bruce > > > On Wed, 27 Oct 2010, [UTF-8] Ørjan Bergmann wrote: > >> I'm also interested in these segmentations for analysis in Matlab. >> >> In particular, which volumes should be loaded to get the coordinates of the >> segmentations? >> >> I assume the segmentation volumes are just indices (all voxel belonging to >> the same segment are assigned the same unique index), correct ? >> >> --- >> Sincerly, >> Dr. Ørjan Bergmann >> >> >> >> On Wed, Oct 27, 2010 at 14:25, Bruce Fischl <fis...@nmr.mgh.harvard.edu >> (mailto:fis...@nmr.mgh.harvard.edu) >> (mailto:fis...@nmr.mgh.harvard.edu)>wrote: >> (mailto:fis...@nmr.mgh.harvard.edu%29%3ewrote:) >> >>> Hi Aya, >>> >>> you should be able to convert our segmentations to Nifti, which I assume >>> Brainvoyager can read. You can load any of our volumes into matlab with >>> either MRIread.m or load_mgh.m and go from there. >>> >>> cheers >>> Bruce >>> >>> >>> On Wed, 27 Oct 2010, Aya Ben Yakov wrote: >>> >>>> Hi >>>> >>>> I used FreeSurfer to automatically segment subcortical structures, and I >>> would now like to transfer the data to Matlab. I am looking for a way to >>> load the coordinates of all structures (or, if it isn't possible, for each >>> structure, by its number) to Matlab, in Talairach coordinates. Is this >>> possible? If so - how can it be done? >>>> >>>> I use BrainVoyager, not FSL, for analysis, and I would like to somehow >>> use the segmentation from FreeSurfer for analysis in Matlab, in combination >>> with data I have from BrainVoyager (the functional data). I don't >>> necessarily need talairach coordinates, but otherwise I'm not sure how it >>> would be possible to convert between FreeSurfer and BrainVoyager. >>>> >>>> Any suggestions? >>>> Thanks! >>>> Aya >>>> >>>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer@nmr.mgh.harvard.edu (mailto:Freesurfer@nmr.mgh.harvard.edu) >>> (mailto:Freesurfer@nmr.mgh.harvard.edu) >>> (mailto:freesur...@nmr.mgh.harvard.edu%29) >>> 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. 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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:freesur...@nmr.mgh.harvard.edu%29) > 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) The information in this e-mail is intended only for the person to whom it is addressed. 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