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Analyze (SPM)

A very simple and useful format for volumes such as tomographic and dynamic studies. Compatibility with the SPM software is our main concern.
scaling factors / quantitation:
Officially there is none. Quantified images are saved as floats unless you specify one of the [-b16 or -b8] options. SPM howerver does use the imd.funused[1] item in the header structure to define a global scaling factor. You must select the special SPM option [-spm] as well as a quantitation option [-qs or -qc] in order to benefit from this entry.
patient/slice orientations:
We do interpret the 'orient' field which speaks about transverse, sagittal or coronal, but always consider it as supine-headfirst! The "flipped" or "unflipped" versions have no meaning for (X)MedCon because the official definition is not clear about the distiction between both. Does "flipped" mean supine or prone; headfirst or feetfirst ... or vice versa? For those who use Analyze for SPM: a proper Analyze image for SPM has a totally reversed coordinate system in relation to (X)MedCon. SPM wants the slices to be oriented as follows:
- transverse in the first place
- X-axis: Left (hand) -> Right (hand)
- Y-axis: Posterior(back) -> Anterior (front)
- Z-axis: Inferior (feet) -> Superior (Head)
(X)MedCon likes to see it patient based. When your files are supine-headfirst-transverse and stored patient based (like with ECAT 951 PET scans); you can use the Analyze reverse option [-ar] to swap all directions and make the slice orientations conform to SPM. In all other cases you should use an image manipulation program to change orientations.
extra notes:
- The format is not capable to store the patient name.
- In the command-line utility you can now specify the [-optspm] option to manually give the "origin" values when converting to Analyze SPM. By the way, for (X)MedCon these values have no meaning.
- SPM Analyze files can use an "offset" value in the header to define an offset in bytes to the voxel data in the image file. To enable it you should give the [-spm] argument option.
Format: Analyze (SPM)  
Color Mapgrayscale, rgb<<]]
File Endianlittle & big
Pixel TypesUint8, Int16, Int32, float, double, rgb, (complex)Int8, Uint16, Uint32, Int64, Uint64
Scaling Factorsquantify & calibrate factors / image are NOT supported
Dimensions / Imagedifferent dimensions for each image are NOT supported
Pixel Types / Imagedifferent pixeltypes for each image are NOTsupported
SPM Remarks
1)imd.funused[0] = the offset
2)imd.funused[1] = one global scaling factor
3)(Int16) dh.originator[0...1][2...3][4...5] = origin (X, Y, Z)
4)patient name will be lost

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Page last modified on January 30, 2007, at 12:14 AM