Summary of what happened:
I am using fMRIprep to process my fMRI data and was hoping to use magnitude and phase data at different echo times of a GRE sequence for the distortion correction. I would like to check that I have uploaded the data in the correct format, as there are a few steps that are unclear to me and the resulting corrected BOLD images appear suboptimal.
My main questions are:
- Have I used constructed the .json files correctly?
- Is the phase data in the correct units?
I am using fMRIprep v23.2.1 and my data is BIDS compliant.
I get the following lines of code which I believe means that fMRIprep is correctly identifying my mag and phase images and will use them to generate the B0 field map:
240725-13:47:00,986 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 1 estimator(s): [<EstimatorType.PHASEDIFF: 3>].
240725-13:47:01,42 nipype.workflow INFO:
Setting-up fieldmap "fmap0" (EstimatorType.PHASEDIFF) with <sub-031_magnitude1.nii.gz, sub-031_magnitude2.nii.gz, sub-031_phase1.nii.gz, sub-031_phase2.nii.gz>
Below shows the contents of the .json files. Do they look correct?
sub-031_magnitude1.json:
{
"EchoTime": 0.00584,
"IntendedFor": [
"func/sub-031_task-rest_run-1_bold.nii"
],
"B0FieldIdentifier": "fmap0"
}
sub-031_magnitude2.json:
{
"EchoTime": 0.01063,
"IntendedFor": [
"func/sub-031_task-rest_run-1_bold.nii"
],
"B0FieldIdentifier": "fmap0"
}
sub-031_phase1.json:
{
"EchoTime": 0.00584,
"IntendedFor": [
"func/sub-031_task-rest_run-1_bold.nii"
],
"B0FieldIdentifier": "fmap0"
}
sub-031_phase2.json:
{
"EchoTime": 0.01063,
"IntendedFor": [
"func/sub-031_task-rest_run-1_bold.nii"
],
"B0FieldIdentifier": "fmap0"
}
These phase maps are wrapped between 0 and 2 pi. The image below shows the data for _phase1.nii.gz
. Is this correct?