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BIC-MNI / minc-tools

Basic minc-tools from former minc repository
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mnc2nii intensity ranges #51

Open lblewis opened 8 years ago

lblewis commented 8 years ago

Hello,

For some select filetypes, the intensity range is not identically maintained between mnc to nii.

Example files:

ftp://bigbrain.loris.ca/BigBrainRelease.2015/3D_Volumes/MNI-ICBM152_Space/mni_icbm152_t1_tal_nlin_sym_09b_hires.mnc ftp://bigbrain.loris.ca/BigBrainRelease.2015/3D_Volumes/MNI-ICBM152_Space/full8_400um_2009b_sym.mnc

mni_icbm152_t1_tal_nlin_sym_09b_hires.mnc is unsigned short 0-65535 with intensity 0-96. mnc2nii outputs .nii with intensity 0-65535 (scaled up):

mnc2nii mni_icbm152_t1_tal_nlin_sym_09b_hires.mnc -unsigned -short mni_icbm152_t1_tal_nlin_sym_09b_hires.nii

full8_400um_2009b_sym.mnc is unsigned byte 0-255 with intensity 0-65535. mnc2nii outputs .nii with intensity 0-255 (scaled down):

mnc2nii full8_400um_2009b_sym.mnc -unsigned -byte full8_400um_2009b_sym.nii

rdvincent commented 8 years ago

@lblewis Thanks. Which version of mnc2nii are you using?

lblewis commented 8 years ago

Vlad's minc-toolkit-v2.

rdvincent commented 8 years ago

@lblewis I think this may actually be a bug in Display's reading of NIfTI files. The NIfTI header looks correct, but Display is showing the wrong thing.

lblewis commented 8 years ago

Ah, I believe you are correct!

gdevenyi commented 8 years ago

Maybe resolved by https://github.com/BIC-MNI/Display/issues/65 ?