This script converts an existing multi-slice image (a UNC, Analyze, NIFTI-2 or DICOM image)
to NIFTI-1 format. Note that
the script runs a more general program called MSIConverter, with
the environment variable OutputType=NIFTI-1, thus producing a
NIFTI-1 format output image.
Running the script without any arguments produces the
following output.
Usage: MSIConverter [options] inputImage1 [inputImage2 inputImage3 ...]
-1,--one-file-per-slice-dicom When saving in DICOM format, writes one DICOM
file per slice of image data.
-?,--help Displays this help message.
-B,--body-part <body-part> Specifies the imaged body part. Must be one of:
HEAD HEADNECK ABDOMEN ABDOMENPELVIS ADRENAL
ANKLE AORTA ARM AXILLA BACK BLADDER BRAIN
BREAST BRONCHUS BUTTOCK CALCANEUS CALF CAROTID
CEREBELLUM CSPINE CTSPINE CERVIX CHEEK CHEST
CHESTABDOMEN CHESTABDPELVIS CIRCLEOFWILLIS
CLAVICLE COCCYX COLON CORNEA CORONARYARTERY
DUODENUM EAR ELBOW ESOPHAGUS EXTREMITY EYE
EYELID FACE FEMUR FINGER FOOT GALLBLADDER HAND
HEART HIP HUMERUS ILEUM IAC JAW JEJUNUM KIDNEY
KNEE LARYNX LEG LIVER LSPINE LSSPINE LUNG
MAXILLA MEDIASTINUM MOUTH NECK NECKCHEST
NECKCHESTABDOMEN NECKCHESTABDPELV NOSE ORBIT
OVARY PANCREAS PAROTID PATELLA PELVIS PENIS
PHARYNX PROSTATE RECTUM RIB SSPINE SCALP
SCAPULA SCLERA SCROTUM SHOULDER SKULL SPINE
SPLEEN STERNUM STOMACH SUBMANDIBULAR TMJ TESTIS
THIGH TSPINE TLSPINE THUMB THYMUS THYROID TOE
TONGUE TRACHEA URETER URETHRA UTERUS VAGINA
VULVA WRIST ZYGOMA.
-b,--dob <date> Specifies the patient's date-of-birth.
-d,--pid <ID> Specifies the patient ID.
-id,--study-id <id> Specifies the study id.
-L,--laterality <laterality> Specifies the image anatomical laterality. Must
be one of: Left Right Both.
-l,--scan-plane <plane> Specifies the most-like scan plane (must be
axial, coronal or sagittal).
-m,--modality <modality> Specifies the imaging modality. Must be one of:
ASMT AU AR BDUS BI BMD CR CT CT CTPROTOCOL DG
DOC DX ECG EPS ES FID GM HC HD IO IO IVOC IVUS
KER KO LS MG MR MR NM OAM OCT OP OPM OPV OPT
OSS OT PLAN PR PT PT PX REG RESP RF RG RTDOSE
RTIMAGE RTPLAN RTRECORD RTSTRUCT RWV SC SEG SM
SMR SR SR STAIN TG US VA XA XC AS CD CF CP CS
DF DM DSA DD EC FA FS LP MA MS OPR ST VF.
-n,--name <name> Specifies the patient name.
-pp,--position <pos> Specifies the Patient Position in the scanner.
Must be one of: HFP HFS HFDR HFDL FFP FFS FFDR
FFDL.
-r,--root <dir> Specifies the root directory for image storage.
Converted images will be stored with the same
directory structure as the input images, but
with the specified root directory. The default
is to store the converted images alongside the
source images.
-s,--one-study Give all converted images the same study
instance UID, study date/time and
frame-of-reference UID
-se,--series-number <integer> Specifies the series number.
-u,--output-type <image-type> Specify the type <image-type> of output image
created. Must be one of: NIFTI-1, NIFTI-2,
Analyze, DICOM, UNC (default [from user
preferences]: NIFTI-1).
-v,--verbose Turns on verbose reporting to System.out.
-ver,--version Prints the software build version, and exits.
System properties:
-DOutputType=type, where type is one of: NIFTI-1 NIFTI-2 Analyze DICOM UNC