The tool to use is: track_transform It should be distributed with the DTK / TrackVis tools.
-Lilla On Wed, 9 Nov 2011, Douglas N Greve wrote: > Hi Paolo, I don't think we have have any tools to apply a matrix to a > trk file. Or maybe I'm wrong? > doug > > paolo wrote: >> Bruce, Doug, Thomas, thank you so much, things are getting slowly >> clearer now >> >> I can try to explain better what i want to do, so that perhaps >> it will be easier for you too to tell what is the best way >> to approach this problem >> >> essentially we have a number of subjects, with already extracted >> white matter fiber tracts (in .trk format) >> The idea was to transform these fibers back to freesurfer space (is >> it the talairach space? in any case, is this what happens by using the >> talairach.xfm matrix?), and then compare them in this space, as, i would >> guess, there is still some sort of deviation from the standard fiber >> pathway. >> >> Is this unreasonable? >> >> also, just for visualization purposes, i was thinking of rendering >> these fibers in their context, but the average brain is, as you point >> out, a bit too blurry. >> Would it make sense here to bring something like MNI152 into the >> freesurfer space, and use this one (and its segmentation) instead of the >> fsaverage as an illustrative atlas in freesurfer space? >> >> Paolo >> >> >> >> On Mon, 7 Nov 2011 11:41:46 -0500 (EST) >> Bruce Fischl <[email protected]> wrote: >> >> >>> Hi Paolo, >>> >>> Are you showing individual subject data in the MNI space, or group >>> average data? In general showing template brains and average data is >>> not a good idea. It misrepresents the spatial localization accuracy >>> of the data. You should try to use averages of the anatomy for groups >>> of tracts of average fmri data or other group stats/data. >>> >>> cheers >>> Bruce >>> >>> On Mon, 7 Nov 2011, Paolo wrote: >>> >>> >>>> I think it is well possible. >>>> And in principle i just wanted to use it for presentation, but the >>>> fsaverage doesnt really look like a "template" brain, rather like >>>> an average >>>> >>>> that's why i was wondering whether there is a more realistic >>>> template available in freesurfer space, or how i can create one >>>> (the idea was to recon-all the MNI152, which to me resembles much >>>> more to a brain) >>>> >>>> would it be the correct approach, or do you have other suggestions? >>>> by the way is it normal that recon-all on mni152 takes just ages to >>>> complete? (>12 hours on an athlon64, dont know exactly how long, i >>>> always stopped it before it finished) >>>> >>>> Paolo >>>> >>>> >>>> On 07-Nov-11 16:03, Thomas Yeo wrote: >>>> >>>>> I am probably wrong, but doesn't the volumetric part of fsaverage >>>>> correspond to MNI305 space rather than MNI152 space? >>>>> >>>>> --Thomas >>>>> >>>>> On Mon, Nov 7, 2011 at 9:00 AM, Bruce >>>>> Fischl<[email protected]> wrote: >>>>> >>>>>> Hi Paolo, >>>>>> >>>>>> I think fsaverage has this in the aseg.mgz. >>>>>> >>>>>> cheers >>>>>> Bruce >>>>>> On Mon, 7 Nov 2011, Paolo wrote: >>>>>> >>>>>> >>>>>>> In the meanwhile i did some research, and it looks like >>>>>>> freesurfer does not use MNI152 as default template, am i right? >>>>>>> it seems that the default template is the fsaverage subject, >>>>>>> which in fact does not look like very realistic. >>>>>>> >>>>>>> >>>>>>> Is there any way to get a realistic brain& segmentation that is >>>>>>> "idealized" enough, and still in talairach space (freesurfer >>>>>>> space)? >>>>>>> >>>>>>> maybe the MNI152 after recon-all and mri_transform to apply back >>>>>>> the transformation? >>>>>>> >>>>>>> i am sorry if these questions look unreasonable, i am new of >>>>>>> freesurfer, and still have problem orienting myself in the >>>>>>> documentation :) >>>>>>> >>>>>>> best, >>>>>>> Paolo >>>>>>> >>>>>>> On 05-Nov-11 00:57, Paolo wrote: >>>>>>> >>>>>>>> Hello >>>>>>>> >>>>>>>> I am a new user of freesurfer. >>>>>>>> I was wondering whether the brain regions for the MNI152 >>>>>>>> dataset are available anywhere (i mean the template brain >>>>>>>> regions for the default MNI152 template). >>>>>>>> >>>>>>>> >>>>>>>> I have also another question: i have the dti fiber tracts >>>>>>>> extracted and computed and already in .trk format. >>>>>>>> I was wondering: to bring them back into the template MNI152 >>>>>>>> space, is it sufficient to apply the talairach.xfm >>>>>>>> transformation matrix to the vertex data, or do i also need to >>>>>>>> use the m3z files (which look like a nonlinear deformation >>>>>>>> field)? >>>>>>>> >>>>>>>> thanks in advance! >>>>>>>> Paolo >>>>>>>> >> >> >> >> _______________________________________________ >> 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. 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