mapVBVD with physiological data extraction

Reads Siemens raw .dat file from NXVA MRI raw data. Tested with XA31A, XA50, XA51 and XA61A data.

This modified version reads physiological data embedded in the .dat file, and interpolates them to sync with ADC time points. Both raw signal and interpolated ones will be stored as a struct in twixobj.PMUdata.

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Author: Philipp Ehses ([email protected])

Input: filename or simply meas. id, e.g. mapVBVD(122) (if file is in same path) Keep empty (mapVBVD() or mapVBVD([])) to open file open dialog. Optional arguments: see below

Output: structure of twix_map_obj with elements (if available):

• .image image scan
• .noise noise scan
• .phasecor phase correction scan
• .phasestab phase stabilization scan
• .phasestabRef0 phasestab. ref. (MDH_REFPHASESTABSCAN && !MDH_PHASESTABSCAN)
• .phasestabRef1 phasestab. ref. (MDH_REFPHASESTABSCAN && MDH_PHASESTABSCAN)
• .refscan parallel imaging reference scan
• .refscanPC phase correction scan for reference data
• .refscanPS phase stabilization scan for reference data
• .refscanPSRef0 phasestab. ref scan for reference data
• .refscanPSRef1 phasestab. ref scan for reference data
• .RTfeedback realtime feedback data
• .vop vop rf data (for pTX systems)

Order of raw data

1. Columns
2. Channels/Coils
3. Lines
4. Partitions
5. Slices
6. Averages
7. (Cardiac-) Phases
8. Contrasts/Echoes
9. Measurements
10. Sets
11. Segments
12. Ida
13. Idb
14. Idc
15. Idd
16. Ide

Optional parameters/flags

• removeOS removes oversampling (factor 2) in read direction
• doAverage performs average (resulting avg-dim has thus size 1)
• ignoreSeg ignores segment mdh index (works basically the same as the average flag)
• rampSampRegrid optional on-the-fly regridding of ramp-sampled readout
• doRawDataCorrect enables raw data correction if used in the acquisition (only works for VB atm)

These and more flags can also be set later, e.g "twix.image.flagRemoveOS = 1"

Examples

twix = mapVBVD(measID);

% return all image-data
image_data = twix.image();
% return all image-data with all singular dimensions removed/squeezed:
image_data = twix.image{''}; % '' necessary due to a matlab limitation
% return only data for line numbers 1 and 5; all dims higher than 4 are
% grouped into dim 5):
image_data = twix.image(:,:,[1 5],:,:);
% return only data for coil channels 2 to 6; all dims higher than 4 are
% grouped into dim 5); but work with the squeezed data order
% => use '{}' instead of '()':
image_data = twix.image{:,2:6,:,:,:};

So basically it works like regular matlab array slicing (but 'end' is not supported). Note that there are still a few bugs with more complicated array slicing (e.g. indices have to be in increasing order; repeated indices not supported).

get unsorted raw data (in acq. order)

image_data = twix.image.unsorted(); % no slicing supported atm

General remarks

The raw data can be obtained by calling e.g. twix.image() or for squeezed data twix.image{''} (the '' are needed due to a limitation of matlab's overloading capabilities). Slicing is supported as well, e.g. twix_obj.image(:,:,1,:) will return only the first line of the full data set (all later dimensions are squeezed into one). Thus, slicing of the "memory-mapped" data objects works exactly the same as regular matlab array slicing - with one exception: The keyword 'end' is not supported.

Overloading of the '()' and '{}' operators works by overloading matlab's built-in 'subsref' function. Matlab calls subsref whenever the operators '()', '{}', or '.' are called. In the latter case, the overloaded subsref just calls the built-in subsref function since we don't want to change the behaviour for '.'-calls. However, this has one minor consequence: There's no way (afaik) to know whether the original call was terminated with a semicolon. Thus, a call to e.g. twix.image.NLin will produce no output with or without semicolon termination. 'a = twix.image.NLin' will however produce the expected result.