BIDS validator error: NIFTI_HEADER_UNREADABLE

Software Support
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1

Hi,

I’ve converted my DICOMs to BIDS and tried to run it through the online BIDs validator. I’m receiving this error: NIFTI_HEADER_UNREADABLE, for quite a few of my files. Here is fslhd performed on one of the identified files:

filename sub-001_ses-01_task-WallyC_run-1_echo-1_bold.nii.gz

sizeof_hdr	348
data_type	UINT16
dim0		4
dim1		64
dim2		64
dim3		48
dim4		653
dim5		1
dim6		1
dim7		1
vox_units	mm
time_units	s
datatype	512
nbyper		2
bitpix		16
pixdim0		-1.000000
pixdim1		3.000000
pixdim2		3.000000
pixdim3		3.000000
pixdim4		2.000000
pixdim5		0.000000
pixdim6		0.000000
pixdim7		0.000000
vox_offset	352
cal_max		0.000000
cal_min		0.000000
scl_slope	1.000000
scl_inter	0.000000
phase_dim	2
freq_dim	1
slice_dim	3
slice_name	Unknown
slice_code	0
slice_start	0
slice_end	0
slice_duration	0.000000
toffset		0.000000
intent		Unknown
intent_code	0
intent_name	
intent_p1	0.000000
intent_p2	0.000000
intent_p3	0.000000
qform_name	Scanner Anat
qform_code	1
qto_xyz:1	-2.995243 -0.031890 0.165836 98.091675 
qto_xyz:2	-0.056566 2.965300 -0.451441 -76.222855 
qto_xyz:3	0.159119 0.453852 2.961199 -67.908783 
qto_xyz:4	0.000000 0.000000 0.000000 1.000000 
qform_xorient	Right-to-Left
qform_yorient	Posterior-to-Anterior
qform_zorient	Inferior-to-Superior
sform_name	Scanner Anat
sform_code	1
sto_xyz:1	-2.995243 -0.031890 0.165834 98.091675 
sto_xyz:2	-0.056566 2.965299 -0.451441 -76.222855 
sto_xyz:3	0.159117 0.453852 2.961199 -67.908783 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 
sform_xorient	Right-to-Left
sform_yorient	Posterior-to-Anterior
sform_zorient	Inferior-to-Superior
file_type	NIFTI-1+
file_code	1
descrip		TE=12;Time=150256.575;phase=1;mb=2
aux_file	Unaliased MB2/PE4/LB

Just for some context, this is a multi-echo acquisition. I used dcm2bids version: 3.2.0, based on BIDS version: v1.9.0.

Any insights would be greatly appreciated!

2

Hi @PhoenixByrne,

Do the images appear okay in image viewers? What version of dcm2niix did you use? Can you make sure you are using the most up to date BIDS validator (e.g., the deno version here: GitHub - bids-standard/bids-validator: Validator for the Brain Imaging Data Structure).

Best,
Steven

3

Hi @Steven,

The images seem ok. I have been running the latest BIDs validator and I used version version “6-May-2025 (v1.0.20250506)” of dcm2niix, which can be found here: Releases · rordenlab/dcm2niix · GitHub.

Many thanks!

4

Can you post the full output from the deno BIDS validator?

5

Here’s what I see:

image
image1528×903 94.9 KB

It’s worth noting that I’ve started some analysis pipeline testing so that is where they are some strange naming conversions in the reported outputs. However, files such as /ses-01/func/sub-001_ses-01_task-WallyC_run-1_echo-4_bold.nii.gz is the raw BIDs data.

Thanks!

6

@PhoenixByrne have you tried the deno version locally? Also you should not be putting processed outputs in raw data folders. What scanner vendor and model are these images from?

7

No I haven’t, it’s hard to get the data out of the university-issued virtual environment I’m working from. The scanner is SIEMENS MAGNETOM 3.0T. I do have the scanning protocol to hand if there’s any further information that you need.

8

Can you not install the deno version on the virtual environment, i.e., via conda/pip?