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?
This might be a bug, but the dimensions looks weird (3 slices and 70 volumes?) - could you share the file?
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?
Maybe email me a private link at email@example.com?
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.
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!
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 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?
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.
Okay. That makes sense. Thank you for clarifying and taking the time to once again respond!