nibabel.parrec¶
Read images in PAR/REC format.
This is yet another MRI image format generated by Philips scanners. It is an ASCII header (PAR) plus a binary blob (REC).
This implementation aims to read version 4.0 through 4.2 of this format. Other versions could probably be supported, but we need example images to test against. If you want us to support another version, and have an image we can add to the test suite, let us know. You would make us very happy by submitting a pull request.
PAR file format¶
The PAR format appears to have two sections:
General information¶
This is a set of lines each giving one key : value pair, examples:
. EPI factor <0,1=no EPI> : 39
. Dynamic scan <0=no 1=yes> ? : 1
. Diffusion <0=no 1=yes> ? : 0
(from nibabel/tests/data/phantom_EPI_asc_CLEAR_2_1.PAR
)
Image information¶
There is a #
prefixed list of fields under the heading “IMAGE INFORMATION
DEFINITION”. From the same file, here is the start of this list:
# === IMAGE INFORMATION DEFINITION =============================================
# The rest of this file contains ONE line per image, this line contains the following information:
#
# slice number (integer)
# echo number (integer)
# dynamic scan number (integer)
There follows a space separated table with values for these fields, each row containing all the named values. Here are the first few lines from the example file above:
# === IMAGE INFORMATION ==========================================================
# sl ec dyn ph ty idx pix scan% rec size (re)scale window angulation offcentre thick gap info spacing echo dtime ttime diff avg flip freq RR-int turbo delay b grad cont anis diffusion L.ty
1 1 1 1 0 2 0 16 62 64 64 0.00000 1.29035 4.28404e-003 1070 1860 -13.26 -0.00 -0.00 2.51 -0.81 -8.69 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
2 1 1 1 0 2 1 16 62 64 64 0.00000 1.29035 4.28404e-003 1122 1951 -13.26 -0.00 -0.00 2.51 6.98 -10.53 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
3 1 1 1 0 2 2 16 62 64 64 0.00000 1.29035 4.28404e-003 1137 1977 -13.26 -0.00 -0.00 2.51 14.77 -12.36 6.000 2.000 0 1 0 2 3.750 3.750 30.00 0.00 0.00 0.00 0 90.00 0 0 0 39 0.0 1 1 8 0 0.000 0.000 0.000 1
Orientation¶
PAR files refer to orientations “ap”, “fh” and “rl”.
Nibabel’s required affine output axes are RAS (left to Right, posterior to Anterior, inferior to Superior). The correspondence of the PAR file’s axes to RAS axes is:
ap = anterior -> posterior = negative A in RAS = P
fh = foot -> head = S in RAS = S
rl = right -> left = negative R in RAS = L
We therefore call the PAR file’s axis system “PSL” (Posterior, Superior, Left).
The orientation of the PAR file axes corresponds to DICOM’s LPS coordinate system (right to Left, anterior to Posterior, inferior to Superior), but in a different order.
Data type¶
It seems that everyone agrees that Philips stores REC data in little-endian format - see https://github.com/nipy/nibabel/issues/274
Philips XML header files, and some previous experience, suggest that the REC data is always stored as 8 or 16 bit unsigned integers - see https://github.com/nipy/nibabel/issues/275
Data Sorting¶
PAR/REC files have a large number of potential image dimensions. To handle
sorting of volumes in PAR/REC files based on these fields and not the order
slices first appear in the PAR file, the strict_sort
flag of
nibabel.load
(or parrec.load
) should be set to True
. The fields
that are taken into account during sorting are:
slice number
echo number
cardiac phase number
gradient orientation number
diffusion b value number
label type (ASL tag vs. control)
dynamic scan number
image_type_mr (Re, Im, Mag, Phase)
Slices are sorted into the third dimension and the order of preference for sorting along the 4th dimension corresponds to the order in the list above. If the image data has more than 4 dimensions these will all be concatenated along the 4th dimension. For example, for a scan with two echos and two dynamics, the 4th dimension will have both echos of dynamic 1 prior to the two echos for dynamic 2.
The``get_volume_labels`` method of the header returns a dictionary containing the PAR field labels for this 4th dimension.
The volume sorting described above can be enabled in the parrec2nii command utility via the option “–strict-sort”. The dimension info can be exported to a CSV file by adding the option “–volume-info”.
Module Attributes
|
PAR header versions we claim to understand |
|
Deprecated; please don't use |
Functions
|
Parse, return any PAR headers from NIfTI extensions in exts_source |
|
Create PARREC image from filename filename |
|
Make maybe mutli-line long_str into one long line |
|
Parse a PAR header and aggregate all information into useful containers. |
|
Vector with True for slices in complete volume, False otherwise |
|
Calculate volume numbers inferred from slice numbers slice_nos |
Classes
|
Initialize PARREC array proxy |
|
PAR/REC header |
|
PAR/REC image |
Exceptions
|
Exception for PAR/REC format related problems. |