BIDS Validator Error-- 'BOLD_NOT_4D'

bids
bids-validator

#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.