why not just use the aseg? it has been cleaned up with the surfaces, so it should represent everything inside the pial surface pretty well.
On 3/2/2020 4:52 PM, Octavian Lie wrote: > 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 _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
