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resample_and_stats.qp
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resample_and_stats.qp
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OutputFolder: OUTDIR
OutputSubFolder: stats
InputFolder: OUTDIR
InputSubFolder: qpdata
InputUseCaseId: True
Debug: False
Processing:
- Load:
data:
# Parameter maps <variable>_<organ>_[<method>]
t1_pancreas_molli.nii.gz:
t1_kidney_molli.nii.gz:
t1_liver_molli.nii.gz:
t2star_pancreas_gre_loglin.nii.gz:
r2star_pancreas_gre_loglin.nii.gz:
t2star_kidney_gre_loglin.nii.gz:
r2star_kidney_gre_loglin.nii.gz:
t2star_liver_gre_loglin.nii.gz:
r2star_liver_gre_loglin.nii.gz:
t2star_pancreas_gre_exp.nii.gz:
r2star_pancreas_gre_exp.nii.gz:
t2star_kidney_gre_exp.nii.gz:
r2star_kidney_gre_exp.nii.gz:
t2star_liver_gre_exp.nii.gz:
r2star_liver_gre_exp.nii.gz:
t2star_pancreas_gre_presco.nii.gz:
r2star_pancreas_gre_presco.nii.gz:
iron_pancreas_gre_presco.nii.gz:
pdff_pancreas_gre_presco.nii.gz:
t2star_kidney_gre_presco.nii.gz:
r2star_kidney_gre_presco.nii.gz:
iron_kidney_gre_presco.nii.gz:
pdff_kidney_gre_presco.nii.gz:
t2star_liver_ideal_presco.nii.gz:
r2star_liver_ideal_presco.nii.gz:
iron_liver_ideal_presco.nii.gz:
pdff_liver_ideal_presco.nii.gz:
fat_fraction.nii.gz:
rois:
# Segmentations seg_<organ>_<segmentation name>
seg_pancreas_t1w.nii.gz:
seg_liver_ideal.nii.gz:
seg_kidney_left_dixon.nii.gz:
seg_kidney_right_dixon.nii.gz:
seg_liver_dixon.nii.gz:
seg_spleen_dixon.nii.gz:
seg_lungs_dixon.nii.gz:
seg_body_cavity_dixon.nii.gz:
seg_abdominal_cavity_dixon.nii.gz:
seg_kidney_all_t1_clean.nii.gz: seg_kidney_all_t1
seg_kidney_cortex_l_t1_clean.nii.gz: seg_kidney_cortex_l_t1
seg_kidney_medulla_l_t1_clean.nii.gz: seg_kidney_medulla_l_t1
seg_kidney_cortex_l_t1_clean.nii.gz: seg_kidney_cortex_l_t1
seg_kidney_medulla_r_t1_clean.nii.gz: seg_kidney_medulla_r_t1
seg_kidney_cortex_r_t1_clean.nii.gz: seg_kidney_cortex_r_t1
vat.nii.gz: seg_vat_dixon
asat.nii.gz: seg_asat_dixon
- Exec:
grid: seg_body_cavity_dixon
output-is-roi: True
seg_subcutaneous_fat_dixon: np.max(seg_body_cavity_dixon - seg_abdominal_cavity_dixon, 0)
# This is needed for naming conventions of parameter maps
- Exec:
grid: t1_kidney_molli
output-is-roi: False
t1_kidney_medulla_l_t1: t1_kidney_molli
t1_kidney_cortex_l_t1: t1_kidney_molli
t1_kidney_medulla_r_t1: t1_kidney_molli
t1_kidney_cortex_r_t1: t1_kidney_molli
- Exec:
grid: seg_kidney_right_dixon
output-is-roi: True
seg_kidney_dixon: np.min(seg_kidney_right_dixon + seg_kidney_left_dixon, 1)
- Resample:
data: seg_liver_dixon
type: data
grid: t1_liver_molli
order: 0
output-name: seg_liver_dixon_regrid_liver_molli
- Resample:
data: seg_liver_dixon
type: data
grid: t2star_pancreas_gre_presco
order: 0
output-name: seg_liver_dixon_regrid_pancreas_gre
- Resample:
data: seg_liver_dixon
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_liver_dixon_regrid_kidney_gre
- Resample:
data: seg_pancreas_t1w
type: data
grid: t2star_pancreas_gre_presco
order: 0
output-name: seg_pancreas_t1w_regrid_pancreas_gre
- Resample:
data: seg_pancreas_t1w
type: data
grid: t1_pancreas_molli
order: 0
output-name: seg_pancreas_t1w_regrid_pancreas_molli
- Resample:
data: seg_spleen_dixon
type: data
grid: t1_liver_molli
order: 0
output-name: seg_spleen_dixon_regrid_liver_molli
- Resample:
data: seg_spleen_dixon
type: data
grid: t2star_liver_ideal_presco
order: 0
output-name: seg_spleen_dixon_regrid_liver_ideal
- Resample:
data: seg_spleen_dixon
type: data
grid: t1_kidney_molli
order: 0
output-name: seg_spleen_dixon_regrid_kidney_molli
- Resample:
data: seg_spleen_dixon
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_spleen_dixon_regrid_kidney_gre
- Resample:
data: seg_kidney_medulla_l_t1
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_kidney_medulla_l_t1_regrid_kidney_gre
- Resample:
data: seg_kidney_cortex_l_t1
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_kidney_cortex_l_t1_regrid_kidney_gre
- Resample:
data: seg_kidney_medulla_r_t1
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_kidney_medulla_r_t1_regrid_kidney_gre
- Resample:
data: seg_kidney_cortex_r_t1
type: data
grid: t2star_kidney_gre_presco
order: 0
output-name: seg_kidney_cortex_r_t1_regrid_kidney_gre
- CalcVolumes:
rois:
- seg_body_cavity_dixon
- seg_abdominal_cavity_dixon
- seg_subcutaneous_fat_dixon
- seg_lungs_dixon
- seg_liver_dixon
- seg_spleen_dixon
- seg_kidney_right_dixon
- seg_kidney_left_dixon
- seg_kidney_dixon
- seg_pancreas_t1w
- seg_liver_ideal
- seg_liver_dixon_regrid_liver_molli
- seg_liver_dixon_regrid_pancreas_gre
- seg_liver_dixon_regrid_kidney_gre
- seg_pancreas_t1w_regrid_pancreas_gre
- seg_pancreas_t1w_regrid_pancreas_molli
- seg_spleen_dixon_regrid_liver_molli
- seg_spleen_dixon_regrid_liver_ideal
- seg_spleen_dixon_regrid_kidney_gre
- seg_spleen_dixon_regrid_kidney_molli
- seg_kidney_all_t1
- seg_kidney_medulla_l_t1
- seg_kidney_cortex_l_t1
- seg_kidney_medulla_l_t1_regrid_kidney_gre
- seg_kidney_cortex_l_t1_regrid_kidney_gre
- seg_kidney_medulla_r_t1
- seg_kidney_cortex_r_t1
- seg_kidney_medulla_r_t1_regrid_kidney_gre
- seg_kidney_cortex_r_t1_regrid_kidney_gre
- seg_vat_dixon
- seg_asat_dixon
units: ml
output-name: seg_volumes
- DataStatistics:
roi: seg_pancreas_t1w
data:
- t1_pancreas_molli
- t2star_pancreas_gre_loglin
- r2star_pancreas_gre_loglin
- t2star_pancreas_gre_exp
- r2star_pancreas_gre_exp
- t2star_pancreas_gre_presco
- r2star_pancreas_gre_presco
- iron_pancreas_gre_presco
- pdff_pancreas_gre_presco
- fat_fraction
data-limits:
t1_pancreas_molli : [400, 1200]
t2star_pancreas_gre_loglin : [2, 100]
t2star_pancreas_gre_exp : [2, 100]
t2star_pancreas_gre_presco : [2, 100]
r2star_pancreas_gre_loglin : [10, 500]
r2star_pancreas_gre_exp : [10, 500]
r2star_pancreas_gre_presco : [10, 500]
pdff_pancreas_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: pancreas_t1w_stats
- DataStatistics:
roi: seg_liver_dixon
data:
- t1_liver_molli
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- t2star_pancreas_gre_loglin
- r2star_pancreas_gre_loglin
- t2star_pancreas_gre_exp
- r2star_pancreas_gre_exp
- t2star_pancreas_gre_presco
- r2star_pancreas_gre_presco
- iron_pancreas_gre_presco
- pdff_pancreas_gre_presco
- fat_fraction
data-limits:
t1_liver_molli : [400, 1200]
t2star_kidney_gre_loglin : [5, 100]
t2star_kidney_gre_exp : [5, 100]
t2star_kidney_gre_presco : [5, 100]
t2star_pancreas_gre_loglin : [5, 100]
t2star_pancreas_gre_exp : [5, 100]
t2star_pancreas_gre_presco : [5, 100]
r2star_kidney_gre_loglin : [10, 200]
r2star_kidney_gre_exp : [10, 200]
r2star_kidney_gre_presco : [10, 200]
r2star_pancreas_gre_loglin : [10, 200]
r2star_pancreas_gre_exp : [10, 200]
r2star_pancreas_gre_presco : [10, 200]
pdff_pancreas_gre_presco : [0, 60]
pdff_kidney_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: liver_dixon_stats
- DataStatistics:
roi: seg_liver_ideal
data:
- t2star_liver_ideal_presco
- r2star_liver_ideal_presco
- iron_liver_ideal_presco
- pdff_liver_ideal_presco
data-limits:
t2star_liver_ideal_presco : [5, 100]
r2star_liver_ideal_presco : [10, 200]
pdff_liver_ideal_presco : [0, 60]
stats: all
exact-median: True
output-name: liver_ideal_stats
- DataStatistics:
roi: seg_spleen_dixon
data:
- t1_kidney_molli
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- t1_liver_molli
- t2star_liver_ideal_loglin
- r2star_liver_ideal_loglin
- t2star_liver_ideal_exp
- r2star_liver_ideal_exp
- t2star_liver_ideal_presco
- r2star_liver_ideal_presco
- iron_liver_ideal_presco
- pdff_liver_ideal_presco
- fat_fraction
data-limits:
t1_kidney_molli : [700, 1500]
t2star_kidney_gre_loglin : [2, 150]
t2star_kidney_gre_exp : [2, 150]
t2star_kidney_gre_presco : [2, 150]
t2star_liver_ideal_loglin : [2, 150]
t2star_liver_ideal_exp : [2, 150]
t2star_liver_ideal_presco : [2, 150]
r2star_kidney_gre_loglin : [6, 500]
r2star_kidney_gre_exp : [6, 500]
r2star_kidney_gre_presco : [6, 500]
r2star_liver_ideal_loglin : [6, 500]
r2star_liver_ideal_exp : [6, 500]
r2star_liver_ideal_presco : [6, 500]
#pdff_kidney_gre_presco : [0, 60]
#pdff_liver_ideal_presco : [0, 60]
stats: all
exact-median: True
output-name: spleen_dixon_stats
- DataStatistics:
roi: seg_kidney_all_t1
data:
- t1_kidney_medulla_l_t1
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- fat_fraction
data-limits:
t1_kidney_medulla_l_t1 : [800, 2000]
t2star_kidney_gre_loglin : [20, 120]
t2star_kidney_gre_exp : [20, 120]
t2star_kidney_gre_presco : [20, 120]
r2star_kidney_gre_loglin : [8, 50]
r2star_kidney_gre_exp : [8, 50]
r2star_kidney_gre_presco : [8, 50]
#pdff_kidney_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: kidney_all_t1_stats
- DataStatistics:
roi: seg_kidney_medulla_l_t1
data:
- t1_kidney_medulla_l_t1
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- fat_fraction
data-limits:
t1_kidney_medulla_l_t1 : [800, 2000]
t2star_kidney_gre_loglin : [20, 120]
t2star_kidney_gre_exp : [20, 120]
t2star_kidney_gre_presco : [20, 120]
r2star_kidney_gre_loglin : [8, 50]
r2star_kidney_gre_exp : [8, 50]
r2star_kidney_gre_presco : [8, 50]
#pdff_kidney_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: kidney_medulla_l_t1_stats
- DataStatistics:
roi: seg_kidney_cortex_l_t1
data:
- t1_kidney_cortex_l_t1
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- fat_fraction
data-limits:
t1_kidney_cortex_l_t1 : [800, 2000]
t2star_kidney_gre_loglin : [20, 120]
t2star_kidney_gre_exp : [20, 120]
t2star_kidney_gre_presco : [20, 120]
r2star_kidney_gre_loglin : [8, 50]
r2star_kidney_gre_exp : [8, 50]
r2star_kidney_gre_presco : [8, 50]
#pdff_kidney_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: kidney_cortex_l_t1_stats
- DataStatistics:
roi: seg_kidney_medulla_r_t1
data:
- t1_kidney_medulla_r_t1
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- fat_fraction
data-limits:
t1_kidney_medulla_r_t1 : [800, 2000]
t2star_kidney_gre_loglin : [20, 120]
t2star_kidney_gre_exp : [20, 120]
t2star_kidney_gre_presco : [20, 120]
r2star_kidney_gre_loglin : [8, 50]
r2star_kidney_gre_exp : [8, 50]
r2star_kidney_gre_presco : [8, 50]
#pdff_kidney_gre_presco : [0, 60]
stats: all
exact-median: True
output-name: kidney_medulla_r_t1_stats
- DataStatistics:
roi: seg_kidney_cortex_r_t1
data:
- t1_kidney_cortex_r_t1
- t2star_kidney_gre_loglin
- r2star_kidney_gre_loglin
- t2star_kidney_gre_exp
- r2star_kidney_gre_exp
- t2star_kidney_gre_presco
- r2star_kidney_gre_presco
- iron_kidney_gre_presco
- pdff_kidney_gre_presco
- fat_fraction
data-limits:
t1_kidney_cortex_r_t1 : [800, 2000]
t2star_kidney_gre_loglin : [20, 120]
t2star_kidney_gre_exp : [20, 120]
t2star_kidney_gre_presco : [20, 120]
r2star_kidney_gre_loglin : [8, 50]
r2star_kidney_gre_exp : [8, 50]
r2star_kidney_gre_presco : [8, 50]
#pdff_kidney_gre_presco : [0, 50]
stats: all
exact-median: True
output-name: kidney_cortex_r_t1_stats
- DataStatistics:
roi: seg_asat_dixon
data:
- fat_fraction
stats: all
exact-median: True
output-name: asat_dixon_stats
- DataStatistics:
roi: seg_vat_dixon
data:
- fat_fraction
stats: all
exact-median: True
output-name: vat_dixon_stats
- Save:
seg_liver_dixon_regrid_liver_molli:
seg_liver_dixon_regrid_pancreas_gre:
seg_liver_dixon_regrid_kidney_gre:
seg_pancreas_t1w_regrid_pancreas_gre:
seg_pancreas_t1w_regrid_pancreas_molli:
seg_spleen_dixon_regrid_liver_molli:
seg_spleen_dixon_regrid_liver_ideal:
seg_spleen_dixon_regrid_kidney_gre:
seg_spleen_dixon_regrid_kidney_molli:
- SaveExtras:
pancreas_t1w_stats: pancreas_t1w_stats.tsv
liver_dixon_stats: liver_dixon_stats.tsv
liver_ideal_stats: liver_ideal_stats.tsv
spleen_dixon_stats: spleen_dixon_stats.tsv
kidney_all_t1_stats: kidney_all_t1_stats.tsv
kidney_medulla_l_t1_stats: kidney_medulla_l_t1_stats.tsv
kidney_cortex_l_t1_stats: kidney_cortex_l_t1_stats.tsv
kidney_medulla_r_t1_stats: kidney_medulla_r_t1_stats.tsv
kidney_cortex_r_t1_stats: kidney_cortex_r_t1_stats.tsv
asat_dixon_stats: asat_dixon_stats.tsv
vat_dixon_stats: vat_dixon_stats.tsv
seg_volumes: seg_volumes.tsv
Cases:
SUBJID: