sct_qc¶

G e n e r a t e Q u a l i t y C o n t r o l ( Q C ) r e p o r t f o l l o w i n g S C T p r o c e s s i n g . Generate Quality Control (QC) report following SCT processing.

usage: sct_qc -i IMAGE -p
              {sct_propseg,sct_deepseg_sc,sct_deepseg_gm,sct_deepseg_lesion,sct_register_multimodal,sct_register_to_template,sct_warp_template,sct_label_vertebrae,sct_detect_pmj,sct_label_utils,sct_get_centerline,sct_fmri_moco,sct_dmri_moco,sct_image_stitch,sct_fmri_compute_tsnr}
              [-s SEG] [-d DEST] [-plane {axial,sagittal}] [-resample RESAMPLE]
              [-text-labels {0,1}] [-custom-labels JSON] [-qc QC]
              [-qc-dataset DATASET] [-qc-subject SUBJECT] [-fps float] [-h]
              [-v <int>]

MANDATORY ARGUMENTS¶

-i

I n p u t i m a g e # 1 Input image #1

-p

P o s s i b l e c h o i c e s : s c t _ p r o p s e g , s c t _ d e e p s e g _ s c , s c t _ d e e p s e g _ g m , s c t _ d e e p s e g _ l e s i o n , s c t _ r e g i s t e r _ m u l t i m o d a l , s c t _ r e g i s t e r _ t o _ t e m p l a t e , s c t _ w a r p _ t e m p l a t e , s c t _ l a b e l _ v e r t e b r a e , s c t _ d e t e c t _ p m j , s c t _ l a b e l _ u t i l s , s c t _ g e t _ c e n t e r l i n e , s c t _ f m r i _ m o c o , s c t _ d m r i _ m o c o , s c t _ i m a g e _ s t i t c h , s c t _ f m r i _ c o m p u t e _ t s n r Possible choices: sct_propseg, sct_deepseg_sc, sct_deepseg_gm, sct_deepseg_lesion, sct_register_multimodal, sct_register_to_template, sct_warp_template, sct_label_vertebrae, sct_detect_pmj, sct_label_utils, sct_get_centerline, sct_fmri_moco, sct_dmri_moco, sct_image_stitch, sct_fmri_compute_tsnr

S C T f u n c t i o n a s s o c i a t e d w i t h t h e Q C r e p o r t t o g e n e r a t e SCT function associated with the QC report to generate

OPTIONAL ARGUMENTS¶

-s

I n p u t s e g m e n t a t i o n o r l a b e l Input segmentation or label

-d

I n p u t i m a g e # 2 t o o v e r l a y o n i m a g e # 1 ( r e q u i r e s a s e g m e n t a t i o n ) , o r o u t p u t o f a n o t h e r p r o c e s s . E x a m p l e : ` s c t _ s t r a i g h t e n _ s p i n a l c o r d ` Input image #2 to overlay on image #1 (requires a segmentation), or output of another process. Example: sct_straighten_spinalcord

-plane

P o s s i b l e c h o i c e s : a x i a l , s a g i t t a l Possible choices: axial, sagittal

P l a n e o f t h e o u t p u t Q C . O n l y r e l e v a n t f o r ` - p s c t _ d e e p s e g _ l e s i o n ` . Plane of the output QC. Only relevant for -p sct_deepseg_lesion.

-resample

M i l l i m e t e r r e s o l u t i o n t o r e s a m p l e t h e i m a g e t o . S e t t o 0 t o t u r n o f f r e s a m p l i n g . Y o u c a n u s e t h i s o p t i o n t o c o n t r o l t h e z o o m o f t h e Q C r e p o r t : h i g h e r v a l u e s w i l l r e s u l t i n s m a l l e r i m a g e s , a n d l o w e r v a l u e s w i l l r e s u l t i n l a r g e r i m a g e s . Millimeter resolution to resample the image to. Set to 0 to turn off resampling. You can use this option to control the zoom of the QC report: higher values will result in smaller images, and lower values will result in larger images.

-text-labels

P o s s i b l e c h o i c e s : 0 , 1 Possible choices: 0, 1

I f s e t t o 0 , t e x t w o n ‘ t b e d r a w n o n t o p o f l a b e l s . O n l y r e l e v a n t f o r ` - p s c t _ l a b e l _ v e r t e b r a e ` . If set to 0, text won’t be drawn on top of labels. Only relevant for -p sct_label_vertebrae.

D e f a u l t : ` ` 1 ` ` Default: 1

-custom-labels

P a t h t o a J S O N f i l e c o n t a i n i n g c u s t o m r e g i o n l a b e l s . O n l y r e l e v a n t f o r ` - p s c t _ l a b e l _ v e r t e b r a e ` . Path to a JSON file containing custom region labels. Only relevant for -p sct_label_vertebrae.

D e f a u l t : ` ` ‘ / h o m e / d o c s / c h e c k o u t s / r e a d t h e d o c s . o r g / u s e r _ b u i l d s / s p i n a l c o r d t o o l b o x / c h e c k o u t s / l a t e s t / s p i n a l c o r d t o o l b o x / r e p o r t s / s c t _ l a b e l _ v e r t e b r a e _ r e g i o n s . j s o n ‘ ` ` Default: '/home/docs/checkouts/readthedocs.org/user_builds/spinalcordtoolbox/checkouts/latest/spinalcordtoolbox/reports/sct_label_vertebrae_regions.json'

-qc

P a t h t o s a v e Q C r e p o r t . Path to save QC report.

D e f a u l t : ` ` ‘ . / q c ‘ ` ` Default: './qc'

-qc-dataset

I f p r o v i d e d , t h i s s t r i n g w i l l b e m e n t i o n e d i n t h e Q C r e p o r t a s t h e d a t a s e t t h e p r o c e s s w a s r u n o n If provided, this string will be mentioned in the QC report as the dataset the process was run on

-qc-subject

I f p r o v i d e d , t h i s s t r i n g w i l l b e m e n t i o n e d i n t h e Q C r e p o r t a s t h e s u b j e c t t h e p r o c e s s w a s r u n o n If provided, this string will be mentioned in the QC report as the subject the process was run on

-fps

T h e n u m b e r o f f r a m e s p e r s e c o n d f o r o u t p u t g i f i m a g e s . O n l y u s e f u l f o r s c t _ f m r i _ m o c o a n d s c t _ d m r i _ m o c o . The number of frames per second for output gif images. Only useful for sct_fmri_moco and sct_dmri_moco.

D e f a u l t : ` ` 5 ` ` Default: 5

MISC ARGUMENTS¶

-v

P o s s i b l e c h o i c e s : 0 , 1 , 2 Possible choices: 0, 1, 2

V e r b o s i t y . 0 : D i s p l a y o n l y e r r o r s / w a r n i n g s , 1 : E r r o r s / w a r n i n g s + i n f o m e s s a g e s , 2 : D e b u g m o d e . Verbosity. 0: Display only errors/warnings, 1: Errors/warnings + info messages, 2: Debug mode.

D e f a u l t : ` ` 1 ` ` Default: 1

Examples:

sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc
sct_qc -i t2.nii.gz -s t2_pmj.nii.gz -p sct_detect_pmj
sct_qc -i t2.nii.gz -s t2_seg_labeled.nii.gz -p sct_label_vertebrae
sct_qc -i t2.nii.gz -s t2_seg.nii.gz -p sct_deepseg_sc -qc-dataset mydata -qc-subject sub-45
sct_qc -i t2.nii.gz -s t2_seg.nii.gz -d t2_lesion.nii.gz -p sct_deepseg_lesion -plane axial