External Email - Use Caution Dear Bruce & All,
Sure, I wanted some advice from the greats before registering pre and posteresection (intrasubject) scans. I tried both registrations on several patient data, bbregister clearly superior to mri_robust_register (used with orig/mgz) for both postresection T1 or T2 registration to FS output, even when using a mask for the resection volume with the latter. The best results were using one hemisphere option (the healthy/nonresected one), and the default or init-fsl for initialization (init-spm and init-rr failed often), smth like bbregister --s subj --mov T1postop.nii --lta register_hemiR.lta --o T1bbr_hemiR_fsl.nii --t1 --rh-only --init-fsl My last question relates to creating a binary mask from pial surfaces, but to include mesial temporal structures (amygdala, hippocampus). I tried the following, but the mris_fill process is killed (OOM) after I upgraded to ubuntu 18.04. Is there another, more straightforward solution for the mask? Thank you, Octavian mris_fill -c -r 1 surf/rh.pial mri/rh.pial.filled.mgz & \ mris_fill -c -r 1 surf/lh.pial mri/lh.pial.filled.mgz & \ mri_concat --combine --i mri/rh.pial.filled.mgz --i mri/lh.pial.filled.mgz --o mri/pial.filled.mgz cd ./mri ; \ mri_binarize --i aseg.mgz --match 5 --match 9 --match 10 --match 14 --match 17 --match 18 --match 19\ --match 25 --match 31 --match 44 --match 48 --match 49 --match 53 --match 54 --match 55 --match 57\ --match 63 --match 86 --match 96 --match 97 --match 105 --match 106 --match 114 --match 115\ --match 195 --match 199 --match 203 --match 204 --match 205 --match 216 --match 222 --match 225\ --match 507 --match 557 --match 1200 --match 1201 --match 1205 --match 1206 --match 2200 --match 2201\ --match 2205 --match 2206 --o hippoamy.mask.mgz & \ fscalc pial.filled.mgz add hippoamy.mask.mgz -o epimask.mgz 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
