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
