# Mtnormalisation clarifying questions in AFD/Fixel walkthrough

**URL:** <https://community.mrtrix.org/t/mtnormalisation-clarifying-questions-in-afd-fixel-walkthrough/1322>\
**Category:** Uncategorized\
**Created:** [November 17, 2017, 7:14pm UTC](https://community.mrtrix.org/t/mtnormalisation-clarifying-questions-in-afd-fixel-walkthrough/1322 "2017-11-17T19:14:00Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![aszymanski](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e36b37/32.png) [@aszymanski](https://community.mrtrix.org/u/aszymanski)\
**Post date:** [November 17, 2017, 7:14pm UTC](https://community.mrtrix.org/t/mtnormalisation-clarifying-questions-in-afd-fixel-walkthrough/1322/1 "2017-11-17T19:14:01Z")

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Hello all,

I have two questions regarding errors I get with mtnormalise. It ran on all of my subjects except for one, which gets  
`mtnormalise: [ERROR] error reading from file "/TEST111717_WMFOD_GRP.nii.gz": /TEST111717_WMFOD_GRP.nii.gz: incorrect data check`

What exactly does incorrect data check mean?

Second question: mtnormalise actually doesn’t seem to work. When I do:  
`mrinfo MTNORMTEST111717_WMFOD.nii.gz -property lognorm_scale`,

I get the message:

`mrinfo: [WARNING] no "lognorm_scale" entries found in "MTNORMTEST111717_WMFOD.nii.gz"`.

Are either of these errors due to the fact that I’m running mtnormalise on nifti files rather than .mif? Would converting all files for the AFD/Fixel walkthrough to .mif help? Thank you very much for your help 👾 !

ETA: MRtrix3 has been updated to 3.0 RC2

ETA2: So I converted one subject to mif just to try it out, and it does look like a nifti issue:

```auto
$ mrinfo wmfod_norm.mif -property lognorm_scale
0.837901473
$ mrinfo MTNORMTEST111717_WMFOD.nii.gz -property lognorm_scale
mrinfo: [WARNING] no "lognorm_scale" entries found in "MTNORMTEST111717_WMFOD.nii.gz"

```

Any possibility of mtnormalise working on nii.gz files in the future?

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**Author:** ![rsmith](https://community.mrtrix.org/user_avatar/community.mrtrix.org/rsmith/32/2672_2.png) [@rsmith](https://community.mrtrix.org/u/rsmith)\
**Post date:** [November 20, 2017, 12:00am UTC](https://community.mrtrix.org/t/mtnormalisation-clarifying-questions-in-afd-fixel-walkthrough/1322/2 "2017-11-20T00:00:09Z")

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Hi Amanda,

> `mtnormalise: [ERROR] error reading from file "/TEST111717_WMFOD_GRP.nii.gz": /TEST111717_WMFOD_GRP.nii.gz: incorrect data check`

That’s emanating from one of [these](https://github.com/MRtrix3/mrtrix3/blob/master/core/file/gz.h#L96) two [lines](https://github.com/MRtrix3/mrtrix3/blob/master/core/file/gz.h#L120). “Incorrect data check” is not a message that _MRtrix3_ is generating, but one it is simply echoing from the GZ file handling library when it encounters an error. So I can only suggest that your file may have been somehow corrupted. One way to test this would be to try to uncompress the `.nii.gz` into a .`nii` using `gunzip`.

> `mrinfo MTNORMTEST111717_WMFOD.nii.gz -property lognorm_scale`

The NIfTI [image format](http://mrtrix.readthedocs.io/en/latest/getting_started/image_data.html#supported-image-formats) is not capable of storing arbitrary key-value pairs in the image header. Therefore, while `mtnormalise` internally writes this parameter to the output image header within the code, that information is immediately lost if the image data are written to a NIfTI image, and there is no way to recover it. This is a fundamental limitation of the NIfTI format. We recommend sticking to the `.mif` format, and exporting to NIfTI explicitly only when data must be imported into some other software, partly for this reason.

If one absolutely insists on using NIfTI, one trick is to use the _MRtrix3_ [config file](http://mrtrix.readthedocs.io/en/latest/getting_started/config.html), specifically two [options](http://mrtrix.readthedocs.io/en/latest/reference/config_file_options.html): `NIfTI.AutoLoadJSON` and `NIfTI.AutoSaveJSON`. This uses sidecar JSON files to store any relevant key-value entries that would have been encapsulated within the image header if the `.mif` format had been used.

Rob

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<div class="post-metadata">

**Author:** ![aszymanski](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e36b37/32.png) [@aszymanski](https://community.mrtrix.org/u/aszymanski)\
**Post date:** [November 20, 2017, 5:39pm UTC](https://community.mrtrix.org/t/mtnormalisation-clarifying-questions-in-afd-fixel-walkthrough/1322/3 "2017-11-20T17:39:56Z")

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Hi Rob,

Thank you very much for the information, it is always helpful 🙂 We are considering switching to `.mif` format due to the fact it is such an integral part of the analyses we want to do (AFD/Fixel analysis).

Thanks again!

A