fmriprep: Failed resampling of BOLD into MNI space - starting with v20.1.1

Hi, we processed a few commonly used datasets, and after we saw the warning for version 20.2.0, I went back to check how many subjects were affected. So, I am posting the information below as it might be useful for others. All the information is for resting state fMRI only.

	affected  / number of subjects on dataset
ukb      38703    / 38703
pnc        0      / 1394
hcp       951     / 1080
cobre     177     / 177
fbirn II   5      / 5

For the datasets that were affected, these are some statistics for their severity.

UKBIOBANK:

 Mean: 0.00518193539885735
 STD: 0.0016678250764811612
 Min: 4.714077218269039e-05
 Max: 0.0899535575234005

HCP

 Mean: 1.6014423472312408e-07
 STD: 1.2199390972215357e-07
 Min: 0.0
 Max: 8.087149296898133e-07

Cobre

 Mean: 0.3328491497572712
 STD: 0.09601558139962757
 Min: 0.09060217156461481
 Max: 0.5646974185071048

fbirn II

 Mean: 0.15869213891835365
 STD: 0.14207928970998107
 Min: 0.0020258594995189623
 Max: 0.3462542458014055

I hope it helps!

Generally, reusing within the same minor version should be okay

@effigies I don’t have an affected file with a severity of 0.0, sorry if what I posted was unclear! I was trying to check for any way my dataset might have been affected despite not seeing any of the artifacts above.

And @CFGEIER --I changed the last 4 lines of the script to the below, which will print severity for each file and should work with earlier than 3.8 python, and saved it as saved_testing_script.py, then ran it using the loop below (hacky but it was the fastest way for me).

if __name__ == "__main__":
    for fname in sys.argv[1:]:
        affected, severity = test(nb.load(fname))
        print(f"{fname} has severity ({severity})")
        if affected:
            print(f"{fname} is affected ({severity})")

Loop:

for sub in `cat $subjectlist`
do
  scans=`find sub-${sub}/ses-01/func/ -iname "sub-${sub}_*_bold.nii.gz"`
  echo $scans
  python saved_testing_script.py $scans
done

Here’s a simple script to test:

#!/usr/bin/env python
import sys
import numpy as np
import nibabel as nb


def test(img):
    zooms = np.array([img.header.get_zooms()[:3]])
    A = img.affine[:3, :3]
    
    cosines = A / zooms
    diff = A - cosines * zooms.T

    return not np.allclose(diff, 0), np.max(np.abs(diff))


if __name__ == "__main__":
    for fname in sys.argv[1:]:
        affected, severity = test(nb.load(fname))
        if affected:
            print(f"{fname} is affected ({severity=})")

Anything below 1e-7 seems safe. Up to 1e-2 seems likely to be fine, but I’d check. Above that, I would not be surprised to see visible artifacts, but again would check.

You should be able to reuse working directories within a minor release series.

In principle it should be safe to reuse the working directory because the nipype graph has changed.

On Fri, Aug 20, 2021, 17:17 Dorota Jarecka @.***> wrote:

I have multiple images from abide studies that seems to be affected. I understand that I should use 20.2.3 and rerun my analysis, but it’s not clear to me if I can use anything from the previous work directory (run with fmriprep20.2.1)

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Correct, that should be fine. Though I’d be interested in a file that showed both affected and a severity of 0. Could you share the first kilobyte of such a file?

Are you simply after a file with severity of 0.0, in which case I have examples of that from publicly accessible data? Or have misunderstood?

Correct, that should be fine. Though I’d be interested in a file that showed both affected and a severity of 0. Could you share the first kilobyte of such a file?