-
Notifications
You must be signed in to change notification settings - Fork 305
Closed
Labels
Description
What happened?
I wanted to try out the Fielmap-less approach despite the fact that a fieldmap was present in our data set. I used the option --ignore fieldmaps --use-syn-sdc
but in the log output I could see that the pepolar polar method was chosen:
B0 field inhomogeneity map will be estimated with the following 1 estimators: [<EstimatorType.PEPOLAR: 2>].
But when I added --force-syn
option in addition to --ignore fieldmaps --use-syn-sdc
, then I could see that the Fieldmap-less option was now chosen:
Option "--ignore fieldmaps" was set, but either "--use-syn-sdc" or "--force-syn" were given, so fieldmap-less estimation will be executed.
221218-22:01:05,494 nipype.workflow INFO:
B0 field inhomogeneity map will be estimated with the following 1 estimators: [<EstimatorType.ANAT: 5>].
What command did you use?
singularity run -B /scratch/jsein/BIDS:/work,$HOME/.templateflow:/opt/templateflow --cleanenv /scratch/jsein/my_images/fmriprep-22.1.0.simg \
--fs-license-file /work/freesurfer/license.txt /work/$study /work/$study/derivatives/fmriprep22.1.0 \
participant --participant-label $sub \
-w /work/temp_data_${study}_22.1.0\
--mem-mb 50000 --omp-nthreads 10 --nthreads 12 \
--fd-spike-threshold 0.5 --dvars-spike-threshold 2.0 --bold2t1w-dof 9 \
--output-spaces MNI152NLin2009cAsym T1w --ignore slicetiming sbref fieldmaps --use-syn-sdc \
--fs-subjects-dir /work/$study/derivatives/fmriprep/sourcedata/freesurfer --debug compcor --track-carbon
What version of fMRIPrep are you running?
22.1.0
How are you running fMRIPrep?
Singularity
Is your data BIDS valid?
Yes
Are you reusing any previously computed results?
FreeSurfer
Please copy and paste any relevant log output.
No response
Additional information / screenshots
Both fields IntendedFor
and B0FieldSource
/ B0FieldIdentifier
were used in this dataset.