北师大发MRI【磁共振成像数据格-13】

DICOM is the most common standard for receiving scans from a hospital.
Data Format
Dicom Viewer
http://www.rubomedical.com/download/in dex.html (free for 50 times)
MRI和fMRI数据存储
Interpreting Voxel Order from Viewer -Difficult
Actually, most viewers go to some effort to read a volume's header file, and orient the view in the most desirable fashion for viewing.
The standard analyze format does not support the neurological orientation
However, the original images which SPM uses can be in any orientation
Data Format
S
R
L
I
MRI和fMRI数据存储
MRI 来自百度文库件体元存储顺序 Slice Orientation names
Sagittal: A-P x S-I plane
S
P
A
I
MRI和fMRI数据存储
MRI 文件体元存储顺序
A number of MRI file formats involve storing voxel intensities as simply a stream of intensity numbers in to a file in some agreed-upon manner. (Examples: Analyze; AFNI).
MRI和fMRI数据存储
Orientation in Viewers
Neurological: "Images are viewed as though looking from the top of the head downward." "Right is right"
MRI和fMRI数据存储
MRI和fMRI数据存储
MRI 文件体元存储顺序
Radiological vs Neurological Voxel Orders
Storage order in Slice orientation 3-Letter
file
“to" Name
R-L within P-A within I-S
48 possible Storage Orders: one example R-L within P-A within I-S (RPI) Voxels ordered from right to left to store a row Rows ordered from posterior to anterior to store a slice Slices stored from inferior to superior to store a volume (slice orientation=“axial”)
MINC http://www.bic.mni.mcgill.ca/software/minc/minc. html
AFNI http://afni.nimh.nih.gov/ Various lab-specific formats NIfTI (pushed by NIH) http://nifti.nimh.nih.gov/
Orientation in Viewers
Notes software that shows patient-right on screenleft is generally said to be using the Radiological convention, whereas showing patient-right on the screen-right is said to be Neurological convention. the Radiological vs Neurological view issue has little necessary tie to the Radiological vs Neurological coordinates issue.
＝
reference (viewing
direction can also
be behind the
patient) "Radiological" convention for
axes, called as LAS (left-
handed system)
+X = L
+Y = A
+Z = S
MRI和fMRI数据存储
L-R within P-A within I-S
"Axial" "Axial"
LAS RAS
Known as
Radiological Neurological
MRI和fMRI数据存储
Orientation in Viewers
"Radiological" and "Neurological" identify two different conventions for the orientation of views of MRI slices. Radiological: "Images are viewed as though looking upward from the feet of the subject." "Right is Left“
When defaults.analyze.flip=1, the Analyze files are stored in radiological orientation from the beginning to the end.
When defaults.analyze.flip=0, the Analyze files are stored in neurological orientation from the beginning to the end.
"medial": towards the middle of the R-L axis, on either side, and "lateral": away from the middle of the R-L axis on either side.
Head orientation reference
Data Format
Data Format
Digital Imaging and Communications in Medicine (DICOM)
A single DICOM file contains both a header (which stores information about the patient's name, the type of scan, image dimensions, etc), as well as all of the image data (which can contain information in three dimensions).
MRIcro
Data Format
Orientation in DICOM
The DICOM coordinate system is the LPS
Data Format
Competing fMRI formats
Analyze/SPM http://www.mayo.edu/bir/PDF/ANALYZE75.pdf
In general terms, voxels are stored in sequence traveling along a row, one row after row another, one slice after slice another.
MRI和fMRI数据存储
MRI 文件体元存储顺序
MRI和fMRI数据存储
MRIcro has done a nice job of orienting the views in desirable way
viewer that shows the raw data order：voxels are ordered (R-L, P-A, I-S)
This leaves you in the dark regarding the actual order of the data in the file, since it's usually not clear what helpful rotation the viewer has applied.
Analyze (7.5) Format
The Analyze coordinate system is the LAS(Radiological orientation)
Data Format
Analyze (7.5) Format
Image Orientation (SPM2)
The SPM2 program is told about the handedness by the defaults.analyze.flip parameter that is specified in the spm_defaults.m file
MRI 文件体元存储顺序 Slice Orientation names
Axial (Transverse): R-L x A-P plane
A
R
L
P
MRI和fMRI数据存储
MRI 文件体元存储顺序 Slice Orientation names
Coronal: R-L x S-I plane
磁共振成像数据格式介绍
04-19-13 龙志颖
MRI和fMRI数据存储
MRI数据存储
3D MPRAGE (T1)
MRI和fMRI数据存储
MRI数据存储空间
Basic Direction Terms (left-right, anteriorposterior, superior-inferior)
Data Format
Analyze (7.5) Format
Analyze images are the primary image format used in SPM up to version SPM2.
It can be used by other software, such as FSL.
MRI和fMRI数据存储
MRI数据存储空间
空间坐标轴 （描述大脑各体元空间位置）
＝
“Neurological” convention for axes, called as RAS (righthanded system) +X = R +Y = A +Z = S
Head orientation
Stores the image data in one file (*.img) and the header data in another file (*.hdr)
Data Format
Analyze (7.5) Format
The image file:
*.img: An uninterrupted array of (unsigned integer, signed short, signed integer, float or double) voxel values.
MRI和fMRI数据存储形式
fMRI数据存储
4D (3 spatial dimensions+1 temporal dimension)
If one session lasts 360 seconds and TR is 3 seconds, we should get 120 scans. Each scan consists of 3D whole brain volume.