mn2nii failure to produce valid NIfTI files

[cmadjar]

I ran mnc2nii on multiple MINC files and none of the files are converting properly. I encounter two types of issues:

1. Conversion of 4D datasets (ASL, BOLD and DWI)

All 4D datasets that I tried mnc2nii on were all converted into files with no brain on it. Min and Max values on the NIfTI files were set to 0. Note, the number of volumes in the NIfTI files correspond to the number of volumes in the MINC files but they are all empty images across time.

2. Conversion of 3D datasets (T1W, T2W, GRE T2, multi-echo T2, fieldmap, FLAIR)

All of the 3D NIfTI files are converted but the images are not well oriented (see one example below for the T2W acquisition).

T2W:

Information about the mnc2nii version used:

Downloaded with MINC toolkit version 1.9.16 for Ubuntu

program: 2.4.02
libminc: 2.4.02
netcdf : 4.5.0 of Jan 17 2018 17:09:58 $
HDF5   : 1.8.20

More detailed information about the files

I append to this issue a zip file with a folder for each modality that I tried mnc2nii on. Each folder contains:

• a text file with the minheader information of the MINC file used to produce the NIfTI files
• a text file with the minchistory information of the MINC file used to produce the NIfTI files
• a text file with the information printed when using the -verbose option of mnc2nii when creating the NIfTI files
• for the 3D volumes, a JPG showing the sagital, coronal and axial orientation of the NIfTI file

test_mnc2nii_only_text_files.zip

I did not append the MINC or NIfTI files due to size constraint but can definitely share them with you if you need access to them. Just let me know.