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fix bug in crop native box (#230)
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This was being interpreted as 52x52x52vox instead of 52x52x52mm (could be a
c3d bug or limitation in the `-pad-to` command. So had to change this
back to voxel definition, 256x256x256vox. This is ok since at least the
voxel resolution can be specified separately in mm.
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akhanf authored Mar 5, 2023
1 parent 6ae3903 commit b9f6e89
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions hippunfold/config/snakebids.yml
Original file line number Diff line number Diff line change
Expand Up @@ -195,8 +195,8 @@ parse_args:
default: '0.2x0.2x0.2mm'

--crop_native_box:
help: 'Sets the bounding box size for the crop native (e.g. cropT1w space). Make this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off (default: %(default)s)'
default: '52x52x52mm'
help: 'Sets the bounding box size for the crop native (e.g. cropT1w space). Make this larger if your hippocampi in crop{T1w,T2w} space are getting cut-off. This must be in voxels (vox) not millimeters (mm). (default: %(default)s)'
default: '256x256x256vox'



Expand Down Expand Up @@ -392,7 +392,7 @@ nnunet_model:
hippb500: trained_model.3d_fullres.Task110_hcp1200_b1000crop.nnUNetTrainerV2.model_best.tar
neonateT1w: trained_model.3d_fullres.Task205_hcp1200_b1000_finetuneround2_dhcp_T1w.nnUNetTrainerV2.model_best.tar

crop_native_box: '52x52x52mm'
crop_native_box: '256x256x256vox'
crop_native_res: '0.2x0.2x0.2mm'

hippdwi_opts:
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