Image not read correctly? about nifti.jl HOT 6 CLOSED

Would you mind sending the hdr to [email protected]? The tests pass for me on 0.4 and I can read my volumes, so I don't really have any idea where to start.

I fixed the warnings that are actually coming from this package in cc8728e. The others are coming from StrPack and would need to be fixed there.

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Hi Simon,

Here is the header file: https://www.dropbox.com/s/lzez4rt26kllnej/Tutr012BigVolLftEar45um_periotic_bw_sub2-nii.hdr?dl=0

Thanks for your help.

Petr

from nifti.jl.

I created a test.img file full of zeros to accompany that hdr and I get the correct size with 0.4.0-dev+3690. What is your versioninfo()?

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Hi Simon,

I have updated my installation of 0.4, unfortunately with a negative result.
_
_ _ ()_ | A fresh approach to technical computing
() | () () | Documentation: http://docs.julialang.org
_ _ | | __ _ | Type "help()" for help.
| | | | | | |/ ` | |
| | || | | | (| | | Version 0.4.0-dev+3723 (2015-03-08 05:30 UTC)
/ |_'|||__'| | Commit b80f7db* (0 days old master)
|__/ | x86_64-w64-mingw32

julia> workspace(); cd("C:/Users/P/Documents/GitHub/VoxelBox.jl"); include("src/
VoxelBox.jl"); cd("examples");

julia> using NIfTI

WARNING: deprecated syntax "(Type=>Integer)[]" at C:\Users\P.julia\v0.4\StrPack
\src\StrPack.jl:25.
Use "Dict{Type,Integer}()" instead.

WARNING: deprecated syntax "{a=>b, ...}" at C:\Users\P.julia\v0.4\StrPack\src\S
trPack.jl:110.
Use "Dict{Any,Any}(a=>b, ...)" instead.

WARNING: deprecated syntax "[a=>b, ...]" at C:\Users\P.julia\v0.4\StrPack\src\S
trPack.jl:300.
Use "Dict(a=>b, ...)" instead.

WARNING: deprecated syntax "[a=>b, ...]" at C:\Users\P.julia\v0.4\StrPack\src\S
trPack.jl:405.
Use "Dict(a=>b, ...)" instead.
WARNING: Dict{K,V}(ks::AbstractArray{K},vs::AbstractArray{V}) is deprecated, use
Dict{K,V}(zip(ks,vs)) instead.
in depwarn at deprecated.jl:40
in call at deprecated.jl:29
in include at boot.jl:249
in include_from_node1 at loading.jl:128
in reload_path at loading.jl:152
in _require at loading.jl:67
in require at loading.jl:51
Warning: New definition
getindex(NIfTI.NIVolume{T,N},Any...) at C:\Users\P.julia\v0.4\NIfTI\src\NIf
TI.jl:500
is ambiguous with:
getindex(AbstractArray{T,N},AbstractArray{T,N}) at abstractarray.jl:478.
To fix, define
getindex(NIfTI.NIVolume{T,N},AbstractArray{T,N})
before the new definition.

julia> ni=niread("Tutr012BigVolLftEar45um_periotic_bw_sub2-nii.hdr");

julia> size(ni.raw)
(409,282,0,0)

julia>

The entire data set has been uploaded to

https://www.dropbox.com/s/ela1dnd71ynxdcn/examples.zip?dl=0

Best regards,

Petr

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I tried on Linux, and this worked fine. I also tried on Windows, and was able to reproduce your output, but while the size is printed wrong, the values are correct, i.e., size(ni, 3) is 202 and size(ni, 4) is 1. This is a known issue caused by a bug in LLVM (JuliaLang/julia#7434) and not something that can be fixed in this package.

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Curious! Thank you very much for your help.

Petr

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