Bruker ParaVision

ParaVision runs Bruker BioSpec and PharmaScan preclinical MRI scanners. A study folder holds one folder per experiment (<expno>/, with acqp and method), each with reconstructions in pdata/<procno>/: the image data 2dseq and its description visu_pars. OpenReadout reads a study, an experiment, a pdata/<procno> folder or a 2dseq file, one image per reconstruction (spectroscopy reconstructions are traces). Derived from brukerapi (MIT, Pilsen MR group), read as documentation, and the corpus; brukerapi is also the reference reader. Provenance: docs/provenance/bruker-paravision.md.

Parameter files

JCAMP-DX-style records ##$Name=value. An array declares its size in brackets (( 2 ), ( 5, 9 )) and continues on the following lines; strings are in angle brackets (<mm>); structures in parentheses ((2, <FG_ECHO>, <Map Type>, 0, 2)); @n*(v) repeats a value; $$ lines are comments. parse never fails: unreadable records are skipped.

2dseq

VisuCoreFrameCount frames of VisuCoreSize samples (x fastest; 2 or 3 core dimensions; 1 for spectroscopy) of VisuCoreWordType (_8BIT_UNSGN_INT, _16BIT_SGN_INT, _32BIT_SGN_INT, _32BIT_FLOAT) in VisuCoreByteOrder. Each frame is scaled by its VisuCoreDataSlope and VisuCoreDataOffs; the values come back float32 (stored × slope + offset), the way brukerapi scales them.

Frames are ordered by the frame groups of VisuFGOrderDesc, the first group varying fastest. Groups become axes:

group	axis
FG_SLICE	Z (a 3-D core already fills Z: then C)
FG_CYCLE, FG_MOVIE	T
every other group (FG_ECHO, FG_DIFFUSION, FG_FLOW, FG_COMPLEX, FG_ISA, …)	C, named by VisuFGElemComment

When the groups do not multiply to the frame count, frames are listed as T and a note says so.

Pixel size: VisuCoreExtent / VisuCoreSize (mm). Z step of 2-D slices: VisuCoreSlicePacksSliceDist, else the distance between the first two VisuCorePositions. VisuCoreOrientation is reported (extra.orientation.matrix, and the plane its third row is closest to); frames stored transposed (VisuCoreTransposition) are returned as stored and check says so.

Spectroscopy (VisuCoreDimDesc spectroscopic) is a trace; its ppm axis is centred on the method’s PVM_FrqWorkPpm and spans VisuCoreExtent, high to low (inferred).

Subject names, IDs, birth dates and the referring user are withheld (extra.personal_data; withheld in the vendor tree).

Vocabulary (every public identifier in openreadout-medical/src/paravision must appear here)

identifier	meaning
ParavisionReader	the reader
FORMAT_ID	the format id, bruker-paravision

info extras

key	meaning
expno, procno	experiment and processing numbers
method, protocol	Method (or VisuAcqSequenceName) and VisuAcquisitionProtocol
word_type, frame_groups, frame_count	the stored data
rescale, stored_pixel_type	slope and offset applied (varies when frames differ)
value_unit	VisuCoreDataUnits
acquisition	repetition_time_ms, echo_time_ms, inversion_time_ms, flip_angle_deg, averages, echo_train_length, imaging_frequency_mhz, scan_time_s, nucleus, receive_coil, field_strength_t (from the 1H frequency)
subject	sex, type, weight_kg, position
orientation	plane, matrix
personal_data	withheld parameters

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How this reader was derived, file by file: provenance log.