mnc2nii treats minc files touched by different minc tools differently

[gdevenyi]

Running into a very weird bug in minc-toolkit/1.9.15:

Example 1:
have brain1.mnc and brain1_mask.mnc
if I do

> mincmask brain1.mnc brain1_mask.mnc brain1_extracted.mnc
> mnc2nii brain1_extracted.mnc brain1_extracted.nii

I get NIFTI file that has the orientation re-arranged (i.e. no longer in the same space)
If instead I do:

> mincmath -mult brain1.mnc brain1_mask.mnc brain1_extracted.mnc
> mnc2nii brain1_extracted.mnc brain1_extracted.nii

Everything is fine

Example 2:
have brain1_mask.mnc

> mnc2nii brain1_mask.mnc brain1_mask.nii

Everything is fine.

> mincmorph -successive DDDDDDDD brain1_mask.mnc brain1_mask_D.mnc
> mnc2nii brain1_mask_D.mnc brain1_mask_D.nii

Same problems as above.

Example of the swapped orientation problem:

[andrewjanke]

HI Gabriel, My punt is a apparent vs file dimension order bug. I'm currently having the same issues with volextents as it seems that what I originally wrote to try to handle this doesn't work anymore: https://github.com/BIC-MNI/minc-widgets/blob/master/volextents/volextents#L108 I'm putting together a test case for this. I would suggest you try this bit of magic on both the input minc files: mincreshape \ -clobber \ -2 \ +direction \ -dimorder zspace,yspace,xspace \ -dimsize xspace=-1 \ -dimsize yspace=-1 \ -dimsize zspace=-1 \ input.mnc output.mnc and see if the problem still exists. If not then it's dimension ordering and (likely) how mnc2nii detects this. a PS: If anyone has a more robust version of what I've used in volextents I'm also all ears!

…

On 20 July 2017 at 06:59, Gabriel A. Devenyi ***@***.***> wrote: Running into a very weird bug in minc-toolkit/1.9.15: Example 1: have brain1.mnc and brain1_mask.mnc if I do > mincmask brain1.mnc brain1_mask.mnc brain1_extracted.mnc > mnc2nii brain1_extracted.mnc brain1_extracted.nii I get NIFTI file that has the orientation re-arranged (i.e. no longer in the same space) If instead I do: > mincmath -mult brain1.mnc brain1_mask.mnc brain1_extracted.mnc > mnc2nii brain1_extracted.mnc brain1_extracted.nii Everything is fine Example 2: have brain1_mask.mnc > mnc2nii brain1_mask.mnc brain1_mask.nii Everything is fine. > mincmorph -successive DDDDDDDD brain1_mask.mnc brain1_mask_D.mnc > mnc2nii brain1_mask_D.mnc brain1_mask_D.nii Same problems as above. Example of the swapped orientation problem: — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[rdvincent]

mnc2nii is pretty buggy. I have been working on some comprehensive fixes, but it is surprisingly hard to catch all of the cases.

[gdevenyi]

@andrewjanke sadly, the mincreshape didn't fix it up :(

[fristed]

This seems to be exactly the same bug we report in issue #32 (last comment). Also, I think this bug arose with the fix done in November 2016, which addressed the issue of wrong start values. Running a mnc2nii from before the November 2016 fix does not have the bug with swapped orientation.
In issue #32 (last comment) I provide an example, which behaves similarly as the example provided by Gabriel above. However, running an old (before Novmeber 2016) version of mnc2nii does not result in the error.

[gdevenyi]

Thanks for the hint @fristed, an older version of mnc2nii doesn't have this bug and otherwise converts everything fine.

[gdevenyi]

Fixed by #99