Hi Ben, please remember to post the list. Answers below On 08/14/2018 02:22 PM, Ben M wrote: > > External Email - Use Caution > > Hi Doug, > > Thanks again for your help! > > | It reslices the mov into the anatomical space. What do you mean when > you "load" them? > > I mean when I view the images in fsleyes they don't seem to be very > different, but I suppose that's because the reslicing is probably very > subtle to see. > > I just came across this post > https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-February/036120.html, > > in which you suggest running > > tkregister2 --mov func.nii --fstarg --reg register.dat --fslregout > fsl.mat --noedit > > to get an FSL-compatible registration. I'd also like to use fnirt, and > for that I need the affine transformation matrix from bbregister. I > think if I simply do: > > $ bbregister --t2 --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --s 001 > $ tkregister2 --mov /data/mean_func.nii.gz --fstarg --reg > /data/bbregister/reg.lta --fslregout /data/fsl.mat --noedit > > tkregister2 will put the transformation matrix reg.lta in the > appropriate format for fnirt, right? Or do I still need to play around > with freesurfer's coordinate system? It should be ok > > Best, > Ben > > > On Mon, Aug 13, 2018 at 10:11 PM, Douglas N. Greve > <dgr...@mgh.harvard.edu <mailto:dgr...@mgh.harvard.edu>> wrote: > > > > On 08/13/2018 03:02 PM, Ben M wrote: > > > External Email - Use Caution > > Hi Doug, > > Thank you very much for your response, it helped me a lot. > I checked the examples of mri_vol2vol and for > functional-to-structural registration I think I should do > > $ bbregister --t2 --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --s 001 > $ mri_vol2vol --lta /data/bbregister/reg.lta --mov > /data/mean_func.nii.gz --fstarg --o func2anat.nii.gz --no-resample > > If I understood correctly, this will align mean_func with the > structural image (orig.mgz I think). Is this correct? > > Yes > > > I have two follow up questions if you don't mind: > > 1 - I'd like to get the file describing the affine > registration of the functional to structural space for > subsequent preprocessing. I think this should be the reg.lta > (or reg.dat) file from the bbregister step, shouldn't it? This > file contains the transformation matrix from functional to > structural, is that correct? > > Yes. You may need info here to decode it: > https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems > <https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems> > > 2 - does mri_vol2vol actually physically move the -mov image? > I think it does, which is the --o func2anat image above. > However when I load the mean_func and func2anat images, they > don't seem to be different in terms of orientation. I suppose > it's because it's difficult to see the transformation with the > naked eye? > > It reslices the mov into the anatomical space. What do you mean > when you "load" them? > > > Best, > Ben > > > > > 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. > >
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