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ex_vivo_pipeline's Introduction

Hello! My name is Zaki,

a student of neuroscience

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ex_vivo_pipeline's Issues

Indentation Error

This is all wrongly indented, possible nvim&vscode problems.

Ex_vivo_Pipeline/DWIpreproc.sh

Lines 114 to 142 in 5464fd6

dwibiascorrect fsl "${previous_DTI}${sub_id}/fslpreproc_data/${new_basename}_concat_denoised_unrang_preproc.mif" "${previous_DTI}${sub_id}/unbias_data/${new_basename}_concat_denoised_unrang_preproc_unbiased.mif" \
-bias "${previous_DTI}${sub_id}/unbias_data/${new_basename}_concat_denoised_unrang_preproc_bias.mif" \
-mask "${my_src_raw}${sub_id}/${sub_mask%.*}_wholebrain_mask_resampled.nii.gz"
dwi2tensor -mask "${my_src_raw}${sub_id}/${sub_mask%.*}_wholebrain_mask_resampled.nii.gz" \
"${previous_DTI}${sub_id}/unbias_data/${new_basename}_concat_denoised_unrang_preproc_unbiased.mif" \
"${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI.nii"
tensor2metric -mask "${my_src_raw}${sub_id}/${sub_mask%.*}_wholebrain_mask_resampled.nii.gz" \
-fa "${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI_FA.nii" \
-ad "${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI_AD.nii" \
-rd "${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI_RD.nii" \
-adc "${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI_MD.nii" \
"${previous_DTI}${sub_id}/tensor_data/${new_basename}_concat_denoised_unrang_preproc_unbiased_DTI.nii"
echo -e "\n-=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=-"
echo "Finished DTI metric extraction"
echo -e "\n-=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=--=-=-=-"
fi
else
echo "Subject ${sub_id} Does not have DWI data"
fi
fi
fi
echo -e "\n============================================================================================"
fi

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