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nipreps / fmriprep

fMRIPrep is a robust and easy-to-use pipeline for preprocessing of diverse fMRI data. The transparent workflow dispenses of manual intervention, thereby ensuring the reproducibility of the results.
https://fmriprep.org
Apache License 2.0
629 stars 291 forks source link

EPI skulls stripping errors #515

Closed chrisgorgo closed 7 years ago

chrisgorgo commented 7 years ago

ds000030

-50013 image

chrisgorgo commented 7 years ago

Note to self: the following combination of procedures generates good results:

N4BiasFieldCorrection -d 3 -i /d/data/hard_masking_cases/sub-10280_task-bart_bold.nii.gz -o /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu.nii.gz
bet /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu.nii.gz /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet.nii.gz -m -f 0.2
3dUnifize -T2 -prefix  /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_unifize.nii.gz   /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet.nii.gz
3dAutomask -dilate 1 -prefix /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_unifize_automask.nii.gz /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_unifize.nii.gz
fslmaths /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_unifize_automask.nii.gz -mul /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_mask.nii.gz /d/data/hard_masking_cases/sub-10280_task-bart_bold_inu_bet_unifize_automask_intersection.nii.gz