ToAnalyze - Convert a MultiSliceImage to Analyze^TM Format

This script converts an existing multi-slice image (a UNC, NIFTI-1, NIFTI-2 or DICOM image) to Analyze^TM format. Note that the script runs a more general program called MSIConverter, with the variable OutputType=Analyze, thus producing an Analyze^TM 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