BIDS Validator Error-- 'BOLD_NOT_4D'

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1

Hello,

I just ran the BIDS Validator (http://bids-standard.github.io/bids-validator/) on my dataset and got the error ‘BOLD_NOT_4D’ evidecned by ‘header field “dim” = 3,112,112,70’. This error suggests that the image is not 4D. However, I have gotten this error in the past and have coded in a conversion check into my script. When I read the nifti header the field ‘dim’ is: [ 4 112 112 70 314 0 0 0] suggesting the image is 4D.

Am I missing something or is there an issue with the validator for this data?

2

This might be a bug, but the dimensions looks weird (3 slices and 70 volumes?) - could you share the file?

3

Hi Chris,

Here is the header info for the file (it is a functional scan):

sizeof_hdr : 348
data_type : b’’
db_name : b’’
extents : 0
session_error : 0
regular : b’r’
dim_info : 57
dim : [ 4 112 112 70 314 0 0 0]
intent_p1 : 0.0
intent_p2 : 0.0
intent_p3 : 0.0
intent_code : none
datatype : int16
bitpix : 16
slice_start : 0
pixdim : [-1. 2. 2. 2. 1. 0. 0. 0.]
vox_offset : 0.0
scl_slope : nan
scl_inter : nan
slice_end : 0
slice_code : unknown
xyzt_units : 10
cal_max : 0.0
cal_min : 0.0
slice_duration : 0.0
toffset : 0.0

I am unable to share the .nii.gz file here. Is there another way of sharing?

4

Maybe email me a private link at chrisgor@stanford.edu?

5

Hi Chris,

Sorry for the confusion but I just looked deeper into this issue and it seems the header info is correct (4D) immediately after conversion with dcm2niix, but once I rename the files in my script to BIDS format and read the header it is incorrect… but only for some. I will have to look into my script/renaming.

Thank you for the quick response and help.

1 Like
6

Hi All,

I received this error ([Code 54] BOLD_NOT_4D), as well as another ([Code 75] NIFTI_PIXDIM4) for 1/15 participants collected from the same site. This topic has been previously discussed in another thread (BIDS Validator Errors: Code 54, Code 66, Code 75) but is seems neither really offer a solution. Any insight is much appreciated!

Nick

7

Hi @nbray005

Thank you for your message! Can you share the header info for this participant? It may also be worth reconverting (presumably from dicom to Nifti) - that appears to have resolved the previous issue.

Thank you,
Franklin

8

Hi @franklin

Thank you very much for taking the time to respond.

I did try to reconvert from DICOM to NIFTI but still had the same result. After diving into this further, and with the help of a colleague, it appears that some DICOM files are simply missing. We are now trying to determine if the data can be recovered. For future reference and to help others, what exactly would I look for in the DICOM Header to help resolve these errors?

Thanks again!

Nick

9

Hi @nbray005

Ahh yep that would do it! This would be looking into the nifti image header and evaluating the dimensions/header information. That is what they did above and found that something was wrong with the conversion because the dimensions didn’t make sense.

Thank you,
Franklin

10

@franklin

Okay. That makes sense. Thank you for clarifying and taking the time to once again respond!

Nick