External Email - Use Caution Dear Bruce, thank you for your replies.
I planned using this line for intrasubject pre to postop (postresection) MRI T1 registration 1. with mri_robust_register: mri_robust_register --mov postop.mgz --dst preop.mgz --lta posttopre.lta --mapmov posttopre.mgz --weights posttopre-weights.mgz --iscale --satit -- maskmov itksnap_rezvol.nii 2. with bbregister bbregister --s sbj --mov postop.mgz --init-fsl --reg register.lta --o posttopre.mgz --t1 Here are follow-up questions and clarifications: 1. With bb register, I do not see an optional flag to accommodate a custom mask volume, such as a mask of the resection volume; if this is true, then one is not required, please advise 2. If one wants to try mri_robust_register for pre to postop MRI alignment, which pre volume from the FS recon pipeline would be indicated for best results? T1.mgz, brain.mgz, or another? 3. With bbregister, which of the several init options (coreg, header, spm, or fsl) are recommended (I have all external packages installed, so that is not an issue), or there is no rule? 4. With mri_robust_register, since the vol of resection is small (sublobar, at most lobar) in size, does a mask of the resection volume for 6 DOF registration improve registration? Or the mask refers more to more partial volumes such as slices, or hemi alignment, as in example 3 here (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_robust_register)? 5. A very rookie question: if one has to use a resection volume mask, do the inside-resection voxels have to be 1, and all outside 0, or the other way around? 6. I then need to mask the coregistered postop volume (posttopre.mgz) with a mask derived from FS preop pipeline, to include all cerebrum (ribbon.mgz) (no cerebellum) but also mesial temporal structures hippocampus/amygdala etc; is there such a mask in the recon pipeline, or it has to be constructed? Thank you, OL On Sun, Feb 23, 2020 at 8:51 PM Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > > Hi Octavian > > 1. Not sure - you should try them. If you have reasonable surfaces I > think bbreg lets you specify masks to ignore, which should be giant help > in this scenario. On the other hand, mri_robust_register does this > automatically. They are both relatively fast so why not try and see? > > 2. Same answer as before. mri_robust_register has flags to tell it to use > an inter-modal similarity function, but you can also tell bbregister it is > a T2 and it should do a good job (and implicitly register to the T1 since > it is already aligned with the surface). > > 3. I'm not sure what you mean - can you explain further? > > cheers > Bruce > > > > On Sun, > 23 Feb 2020, Octavian Lie wrote: > > > External Email - Use Caution > > > > Dear All, > > > > I need to register: > > 1. T1.mgz to a T1 postresection volume (no contrast), with large > > resection. Which one should I use, mri_robust_register, or bbregister, > > if the latter, which is the better initiator (nmi, spm, fsl)? > > > > 2. T1.mgz to a 3D FLAIR SPACE sequence (outside of the flair space > > recon-all flag), which FS registration tool should I use? > > > > 3. I then need to mask the coregistered T1 postresection with a T1.mgz mask. > > > > I would appreciate commands (either names, or full command lines), > > please advise. > > > > Thank you, > > Octavian > > > > _______________________________________________ > > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
