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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>_[<method>]
t1.nii.gz:
t2star_loglin.nii.gz:
r2star_loglin.nii.gz:
t2star_exp.nii.gz:
r2star_exp.nii.gz:
rois:
# Segmentations seg_<organ>_<segmentation name>
seg_kidney_medulla_l_t1.nii.gz:
seg_kidney_cortex_l_t1.nii.gz:
seg_kidney_medulla_r_t1.nii.gz:
seg_kidney_cortex_r_t1.nii.gz:
seg_kidney_r_t2w.nii.gz:
seg_kidney_l_t2w.nii.gz:
seg_kidney_t2w.nii.gz:
- Resample:
data: seg_kidney_medulla_l_t1
type: data
grid: t2star_loglin
order: 0
output-name: seg_kidney_medulla_l_t1_regrid_t2star
- Resample:
data: seg_kidney_cortex_l_t1
type: data
grid: t2star_loglin
order: 0
output-name: seg_kidney_cortex_l_t1_regrid_t2star
- Resample:
data: seg_kidney_medulla_r_t1
type: data
grid: t2star_loglin
order: 0
output-name: seg_kidney_medulla_r_t1_regrid_t2star
- Resample:
data: seg_kidney_cortex_r_t1
type: data
grid: t2star_loglin
order: 0
output-name: seg_kidney_cortex_r_t1_regrid_t2star
- CalcVolumes:
rois:
- seg_kidney_medulla_l_t1
- seg_kidney_cortex_l_t1
- seg_kidney_medulla_l_t1_regrid_t2star
- seg_kidney_cortex_l_t1_regrid_t2star
- seg_kidney_medulla_r_t1
- seg_kidney_cortex_r_t1
- seg_kidney_medulla_r_t1_regrid_t2star
- seg_kidney_cortex_r_t1_regrid_t2star
- seg_kidney_l_t2w
- seg_kidney_r_t2w
- seg_kidney_t2w
units: ml
output-name: seg_volumes
- DataStatistics:
roi: seg_kidney_medulla_l_t1
data:
- t1
- t2star_loglin
- t2star_exp
- r2star_loglin
- r2star_exp
data-limits:
t1 : [1100, 2300]
t2star_loglin : [5, 100]
t2star_exp : [5, 100]
r2star_loglin : [10, 200]
r2star_exp : [10, 200]
stats: all
exact-median: True
output-name: kidney_medulla_l_t1_stats
- DataStatistics:
roi: seg_kidney_medulla_r_t1
data:
- t1
- t2star_loglin
- t2star_exp
- r2star_loglin
- r2star_exp
data-limits:
t1 : [1100, 2300]
t2star_loglin : [5, 100]
t2star_exp : [5, 100]
r2star_loglin : [10, 200]
r2star_exp : [10, 200]
stats: all
exact-median: True
output-name: kidney_medulla_r_t1_stats
- DataStatistics:
roi: seg_kidney_cortex_l_t1
data:
- t1
- t2star_loglin
- t2star_exp
- r2star_loglin
- r2star_exp
data-limits:
t1 : [1100, 2300]
t2star_loglin : [5, 100]
t2star_exp : [5, 100]
r2star_loglin : [10, 200]
r2star_exp : [10, 200]
stats: all
exact-median: True
output-name: kidney_cortex_l_t1_stats
- DataStatistics:
roi: seg_kidney_cortex_r_t1
data:
- t1
- t2star_loglin
- t2star_exp
- r2star_loglin
- r2star_exp
data-limits:
t1 : [1100, 2300]
t2star_loglin : [5, 100]
t2star_exp : [5, 100]
r2star_loglin : [10, 200]
r2star_exp : [10, 200]
stats: all
exact-median: True
output-name: kidney_cortex_r_t1_stats
- Save:
seg_kidney_medulla_l_t1_regrid_t2star:
seg_kidney_medulla_r_t1_regrid_t2star:
seg_kidney_cortex_l_t1_regrid_t2star:
seg_kidney_cortex_r_t1_regrid_t2star:
- SaveExtras:
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
seg_volumes: seg_volumes.tsv
Cases:
SUBJID: