mapVBVD with physiological data extraction

Reads Siemens raw .dat file from VB/VD MRI raw data.

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.