Detect bogus BrainVoyager NIfTI headers

[neurolabusc]

The NIfTI specification defines cal_min and cal_max as follows:

float cal_max;       /*!< Max display intensity */  /* float cal_max;       */
float cal_min;       /*!< Min display intensity */  /* float cal_min;       */

It is standard convention to set both to zero if they are to be ignored. Unfortunately, BrainVoyager seems to set these to 0 and 255 respectively when creating NIfTI data.

The BIDS format BrainVoyager Getting Started Guide (GSG) files exhibit this, e.g. GSGData.zip. Consider the fMRI image that has a mean intensity of 4022 (with a range of 0..49183). Here the cal_min and cal_max of 0..255 is inappropriate, with even dark air voxels having values ~700.

$ fslinfo sub-01_ses-04_task-blocked_run-1_bold.nii.gz   
data_type	FLOAT32
dim1		100
dim2		100
dim3		64
dim4		291
datatype	16
pixdim1		2.000000
pixdim2		2.000000
pixdim3		2.000000
pixdim4		2.000000
cal_max		255.000000
cal_min		0.000000
file_type	NIFTI-1+
$ fslstats sub-01_ses-04_task-blocked_run-1_bold.nii.gz -m -R
4021.941837 0.000000 49183.000000 

It would be great if BrainVoyager could fix this, but bvlabel could also provide a mechanism for detecting and fixing existing bogus values.

[ofgulban]

@neurolabusc thanks a lot for opening this issue and informing us. I will submit this as a bug to brainvoyager.

Just to double check if I understand correctly, here you are talking about a file (probably a .fmr) that is exported from BrainVoyager as nifti (using the GUI export nifti option), right?

[ofgulban]

Tagging @ju-ec and @nausikaa8 , because this might be something to consider while updating the docs and example data.

[nausikaa8]

Thanks @ofgulban, we have updated the tests.