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Error in saving output when is .nii.gz #1532
The environment in which I found this bug are:
I found a problem with some commands (mrresize and mrconvert) when the output specified is .nii.gz format.
To be specific the commands used are:
What happens is that the commands execution proceed without failing (decompression(if needed) - computation - compression), but in the end the saved file is just 8KB whatever is the input size. By checking the file with fslinfo the header is correct. Hence, I guess that the 8KB is just the size of the header.
As additional test I tried to split the execution of the command and the gzip compression. Thus:
If you need some more information, let me know
Thanks for reporting. Unfortunately I can't reproduce on either of my systems (MSY2 on Windows 10, and Arch Linux), for either of the commits you point to. Also, if there was such a glaring issue in our code, I'd be surprised not to have heard about it before. So I'm tempted to think there's something odd about your system, but the fact that you encounter this issue on two different OS's is troubling.
Can you post the contents of your
Also, does running with
I was a surprised too about this "glaring" issue. However, the fact I was sure it happened in two different computers convinced me to report it.
On mac os I've done a trial right now and I haven't encountered any problem.
I don't have the mrtrix config file in any of the systems.
The problem still alive on Ubuntu 16.04 LTS:
mrconvert -debug GM.mif ~/GM.nii.gz
ll -h ~/GM.nii.gz
mrresize -debug -voxel 2.5 nodif_brain_mask.nii.gz ~/nodif_brain_mask_2.5mm.nii.gz
ll -h ~/nodif_brain_mask_2.5mm.nii.gz
Do you have any ideas on what I should check?
Ok, good to hear, that means the issue is likely down to your
This should report all libraries that
this the output of the command:
p.s. I noted that I have a general problem in this system with the creation of gzip archive (for example I'm having problem with FSL first_flirt, which create a .nii.gz file and again it results only the header), maybe there is some corrupted library. If you have hints let me know.
Relevant line is:
This is not the standard version supplied by your distribution. The