Hi Kareem, can you explain a bit more about where these atlas-derived labeling comes from? Is it in MNI space? Is there any reason to think it will register well to this subject? Or is it in this individual's space? If the latter, you probably want to give -t2 to bbregister since in your case as I understand it the gray matter is bright (e.g. 1) and the white matter is dark (0?). Is that correct?
cheers Bruce On Mon, 30 May 2011 k...@rice.edu wrote: > Hi Doug, > > The bbregister didn't work out well, it didn't register properly but I > must be putting in some erroneous argument: > > bbregister --s SUBJ1 --mov TP.nii.gz --reg register.dat --init-fsl --t1 > > The final check with tkregister shows the temporal pole mask several > slices off bilaterally and rotated about 30-40 degrees CW and also > rotated spatially from frontal to posterior brain. > > I also tried a flirt command in FSL but couldn't not get a proper 4x4 > affine matrix to use. Any ideas on why the registration isn't working? > > Thank you, > Kareem > > > Quoting Douglas Greve <gr...@nmr.mgh.harvard.edu>: > >> You use bbregister to compute the registration. You will need a >> template for your atlas (eg, an average anatomy). >> >> doug >> >> On 5/27/11 7:09 PM, k...@rice.edu wrote: >>> Do I feed the registration matrix into another FS command or does >>> bbregister use the reg matrix to transform the atlas mask into FS >>> anatomical space? I will try the bbregister with 12 DOF as you >>> recommend too. >>> >>> Thank you, >>> Kareem >>> >>> >>> Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>> >>>> Yes, there's no other way for FS to know where data should go -- >>>> it has no idea how you derived the input. You can try using >>>> bbregister with 12 DOF to register the atlas template to the FS >>>> anatomical. This will give you a registration matrix. Check it >>>> visually to make sure that it is reasonably accurate. >>>> >>>> doug >>>> >>>> k...@rice.edu wrote: >>>>> Hmm, well I derived the volume from an FSL atlas which I >>>>> exported, binarized, then fed into the commands I listed >>>>> initially. Do I need to register the temporal pole volume to some >>>>> FS space? And how would I so? >>>>> >>>>> Best, >>>>> Kareem >>>>> >>>>> >>>>> >>>>> Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>>> >>>>>> Then it means that the registration is incorrect. How did you >>>>>> create the reg? >>>>>> >>>>>> k...@rice.edu wrote: >>>>>>> No it doesn't look right. It is supposed to map on to the >>>>>>> temporal pole but doesn't do so. I don't think it's in the >>>>>>> right space. Is there a command we are perhaps missing to bring >>>>>>> it to native FS space? >>>>>>> >>>>>>> Best, >>>>>>> Kareem >>>>>>> >>>>>>> >>>>>>> Quoting Douglas N Greve <gr...@nmr.mgh.harvard.edu>: >>>>>>> >>>>>>>> It looks like your commands are correct. When you load >>>>>>>> mask.surf.nii.gz onto the surface, does it look ok? >>>>>>>> >>>>>>>> doug >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> k...@rice.edu wrote: >>>>>>>>> Hello, >>>>>>>>> >>>>>>>>> I've derived a .nii.gz atlas-based volume for a specific part >>>>>>>>> of the cortical surface. I've binarized the volume and now I >>>>>>>>> want to convert the file to a .label file that I can use to >>>>>>>>> identify particular vertices in native FS space for that >>>>>>>>> same subject. >>>>>>>>> >>>>>>>>> This is what I have tried so far: >>>>>>>>> >>>>>>>>> >>>>>>>>> mri_vol2surf --src mask.nii.gz --srcreg /tmp/reg.dat --surf >>>>>>>>> pial --projfrac 0.5 --hemi lh --out mask.surf.nii.gz >>>>>>>>> >>>>>>>>> mri_cor2label --i mask.surf.nii.gz --id 1 --l mask.label >>>>>>>>> --surf SUBJ1 lh pial >>>>>>>>> >>>>>>>>> However when I overlayed the .label onto SUBJ1 the vertices >>>>>>>>> did not match up and was completely off the region of >>>>>>>>> interest on the cortical surface. >>>>>>>>> >>>>>>>>> Does anyone know how to fix this or how to proceed with >>>>>>>>> conversion differently? >>>>>>>>> >>>>>>>>> Thank you very much, >>>>>>>>> Kareem >>>>>>>>> >>>>>>>>> _______________________________________________ >>>>>>>>> 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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> 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. >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>> >>>>>> -- >>>>>> 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 >>>>>> >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> -- >>>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
