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m-reuter
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May 26, 2026 13:03
m-reuter
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m-reuter
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Jul 29, 2026
| cmd="$cmd --noit" | ||
| t1=${SUBJECTS_DIR}/$tid/mri/orig.mgz | ||
| cmd="$cmd --template $t1" | ||
| cmd="$cmd --template $t1 $device_opt" |
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| cmd="$cmd --template $t1 $device_opt" | |
| cmd="$cmd --template $t1" |
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device not needed here, as we are not registering, only mapping, which happens on the CPU.
m-reuter
commented
Jul 29, 2026
| networkx==3.6.1 | ||
| neurolit==0.6.1 | ||
| neuroreg==0.6.2 | ||
| neuroreg==0.10.1 |
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| neuroreg==0.10.1 | |
| neuroreg==0.10.4 |
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In order to remove the FreeSurfer dependencies in the seg_only path, we replace
mri_coreg,mri_robust_register,mri_robust_template,mri_vol2vol,mri_mask,mri_binarize,mri_info) calls withneuroreg.--keep-dtypewe can keep the input data type to replicate FreeSrufer's behaviourmri_robust_register --cost nmias we now use neuroreg.coreg which also replacesmri_coregat the same time (cross modal registration based on NMI and Powell optimiser).In the future, we can generate quick WM surfaces based on the segmentaiton and then can explore if
neuroreg bbregadds any value here.