Hi there,
My team and I are trying to understand what might be causeing some issues we are seeing with susceptability distorion correction. We collected field maps and used those to estimate inhomogeneity. In some, not all, of our participants, we are seeing that the “corrected” image has drastic changes in intensity - which also in some cases messes with the brain mask.
Compared to the original “distorted” image:
This is the B0 map:
We are not sure what is causing this. But in some testing, we reran this person through fMRIprep using the same version and the same command/options and curiously, we got a different result:
Corrected:
Distorted:
B0 map:
Any thoughts/ideas would be helpful!!!
Hi Nikki,
This reminds me of a long debated/repeated issue in fmriprep version 21.x to 23.1.x:
opened 11:08PM - 22 May 23 UTC
closed 01:25PM - 21 Nov 23 UTC
bug
### What happened?
Dear community,
we are using FMRIPREP for the preprocessi… ng of task-based fMRI data. Apparently, the brain mask is not very accurate and the fMRI data is even more distorted after the susceptibility distortion correction (see image attached).
Thank you very much for your help!
### What command did you use?
```shell
docker run -ti --rm \
-u $(id -u):$(id -g) \
-v /data/dataPreproc/rawdata:/data:ro \
-v /data/dataPreproc/derivatives/fmriprep-preprocessing/:/out \
-v /data/dataPreproc/workingDirectory/:/workDir \
-v /home/christian.schmitz/license.txt:/opt/freesurfer/license.txt \
nipreps/fmriprep:latest /data /out \
participant --participant-label "${sub}" \
--output-spaces MNI152NLin6Asym:res-2 MNI152NLin2009cAsym fsLR \
-w /workDir \
--return-all-components \
--cifti-output \
--mem 52000;
```
### What version of fMRIPrep are you running?
23.0.2
### How are you running fMRIPrep?
Docker
### Is your data BIDS valid?
Yes
### Are you reusing any previously computed results?
No
### Please copy and paste any relevant log output.
_No response_
### Additional information / screenshots
These issues were resolved with 23.2.x : What’s new — fmriprep version documentation
Can you run a clean, from scratch (with removing work/tmp) latest fMRIprep on the subjects that you have an issue with?
Amir
