diff --git a/scripts/process_data_dcm-zurich.sh b/scripts/process_data_dcm-zurich.sh index b3c25ba..5508990 100644 --- a/scripts/process_data_dcm-zurich.sh +++ b/scripts/process_data_dcm-zurich.sh @@ -191,25 +191,19 @@ else echo "${SUBJECT}: ${sex}" # TODO: test without angle correction too - # Compute compression morphometrics for diameter_AP with and without normalization to PAM50 - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -o ${PATH_RESULTS}/${file_t2_ax}_diameter_AP_norm.csv - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 0 -o ${PATH_RESULTS}/${file_t2_ax}_diameter_AP.csv - - # Compute compression morphometrics for cross-sectional area with and without normalization - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric area -o ${PATH_RESULTS}/${file_t2_ax}_area_norm.csv - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 0 -metric area -o ${PATH_RESULTS}/${file_t2_ax}_area.csv - - # Compute compression morphometrics for diameter_RL with and without normalization - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric diameter_RL -o ${PATH_RESULTS}/${file_t2_ax}_diameter_RL_norm.csv - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 0 -metric diameter_RL -o ${PATH_RESULTS}/${file_t2_ax}_diameter_RL.csv - - # Compute compression morphometrics for eccentricity with and without normalization - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric eccentricity -o ${PATH_RESULTS}/${file_t2_ax}_eccentricity_norm.csv - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 0 -metric eccentricity -o ${PATH_RESULTS}/${file_t2_ax}_eccentricity.csv - - # Compute compression morphometrics for solidity with and without normalization - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric solidity -o ${PATH_RESULTS}/${file_t2_ax}_solidity_norm.csv - sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 0 -metric solidity -o ${PATH_RESULTS}/${file_t2_ax}_solidity.csv + # Compute morphometric measures normalized to PAM50 template space + # Note: CSV file without normalization is also generated automatically + # Note: morphometric measures for individual subjects are appended to a single CSV file + # diameter_AP + sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -o ${PATH_RESULTS}/compression_metrics.csv + # cross-sectional area + sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric area -o ${PATH_RESULTS}/compression_metrics.csv + # diameter_RL + sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric diameter_RL -o ${PATH_RESULTS}/compression_metrics.csv + # eccentricity + sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric eccentricity -o ${PATH_RESULTS}/compression_metrics.csv + # solidity + sct_compute_compression -i ${file_t2_ax_seg}.nii.gz -vertfile ${file_t2_ax_seg}_labeled.nii.gz -l ${file_compression}.nii.gz -normalize-hc 1 -sex ${sex} -metric solidity -o ${PATH_RESULTS}/compression_metrics.csv fi fi