Question of crop and preprocess quality #392
qiudashuai1
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Hi, The QC report you are showing looks fine for inhomogeneity correction. You will also have to inspect the registration reports. |
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Hi, I have preprocessed my data using the following command :
sudo docker run -it --rm --user $(id -u)
-v $PWD/input_BIDS:/input_BIDS:ro
-v $PWD/preprocess_outputs:/preprocess_outputs/
ghcr.io/cobralab/rabies:latest -p MultiProc preprocess /input_BIDS/ /preprocess_outputs/ --apply_STC --TR 2 --bold_autobox --commonspace_reg masking=true,brain_extraction=false,template_registration=SyN,fast_commonspace=false
My data contains excessive neck tissue, so I used the --bold_autobox option to crop the data. However, it appears to be the same as the uncropped data. Is there have other recommended method to crop the brain? Additionally, the preprocessed data has some artifacts. I have limited knowledge about mouse fMRI. Is this preprocessing quality correct?
This is my origin data
This is the preprocessed data
And the QC image
rabies_preprocess.log
sub-con1_task-rest_bold_RAS_autobox_inho_cor.nii.gz
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