BIDS Validator error - code: 55 - JSON_SCHEMA_VALIDATION_ERROR : SliceTiming should be >= 0

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1

Hello everyone!

I want to use fmriprep but I have some issues. I have this BIDS error and i don’t really know how to fix it.
I have different slicetiming in my func files and some of them are negative.
For example for the task 01 I have this :
“SliceTiming” : [
2.0425;
1.9875;
1.9325;
1.8775;
…
…
0.11;
0.055;
0 ],

For the task02 I have :
“SliceTiming” : [
0;
-0.055;
-0.11;
-0.165;
…
…
-1.9325;
-1.9875;
-2.0425 ],

Also, i cant’ use the command “–ignore slicetiming” : It says that I still have the same issue during the bids validator.
I’m wondering if maybe I could ignore the bids validator.

Thank you very much for your help,

Audrey

2

Audrey

To understand your problem, can you tell me the Conversion Software used to create this file, and the version. If the files were generated by dcm2niix:

"ConversionSoftware": "dcm2niix",
"ConversionSoftwareVersion": "v1.0.20200331"

I suspect this reflects one of the two issues described here:

  1. The conversion software looked at the first volume of the series for slice times, and some sequences (e.g. early CMRR sequences) inserted bogus values into the first DICOM volume. The solution is to retireve slice times from subsequent volumes. Modern versions of dcm2niix will do this.
  2. The user acquired data using Siemens motion correction (MoCo) option, and Siemens notes that The motion correction images are in anatomic order, while the non-moco data are in descending order, so the latest time is subtracted from each acquisition time resulting in the negative values. A converter should be aware of this. Again, use a modern version of dcm2niix and look at the output. In general, I would strongly urge against using MoCo, and if both non-MoCo and MoCo data were saved you want to analyze the non-MoCo data. The MoCo data will hide motion from subsequent analyses, so you can not model it as a regressor. Likewise, you may not be able to detect the true magnitude of motion, making it impossible to censor motion. I would only recommend MoCo for real time clinical studies. Scientists can do much better with offline correction.
3

Thank you very much for your anwer!

I used dcm2niix to convert my data from DICOM to nifti but you were right; I used a old version which is the v1.0.20181125

I converted my DICOM files again with the latest release v1.0.20200331 and it worked!

Thank you very much for your help !