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 <fis...@nmr.mgh.harvard.edu> 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<fis...@nmr.mgh.harvard.edu> 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 > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu 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.
