Combining RDA Files

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1

Hi legends,
I was hoping some advice about some old data I am trying to process. It’s MEGA-PRESS data which they’ve only saved using RDA files, with the scan broken up midway. I.e. 128 transients in one run and then 128 transients in another run, so 4 RDA files (2 on, 2 off).
Any advice on how to combine these? I can get Osprey to read the data within a run, but not with the 4 in a folder.
I appreciate RDA is not ideal but it’s what we’ve got.
Thanks in advance!

2

Hi @marilena,

Depends on how you’re going to process the data. Gannet allows you to join separate acquisitions.

Mark

3

Hi @mmikkel
Thanks - happy to use Gannet but haven’t had much luck joining the RDA files in it?

sub02={
    'off_1.rda',...
    'on_1.rda',...
    off_2.rda',...
    'on_2.rda'};

metab=[sub02(:)]
MRS=GannetLoad(metab);
MRS=GannetFit(MRS);

with MRS_struct.p.join = 1;

Updating results in MRS_struct_vox1.mat...
Unrecognized field name "spec".

Error in GannetFit (line 55)
freq = MRS_struct.spec.freq;

Error in TestGannet (line 16)
MRS=GannetFit(MRS);

Is what happens with the old RDA files. If I don’t run them in join they load/fit OK.

New RDA files don’t read into Gannet correctly (with or without join on).
I think the header structure moved.

image
image377×184 9.83 KB

Thanks in advance!!

4

You could convert each using spec2nii spec2nii rda path/to/each/file.rda, then merge them using the NIfTI-MRS command line tools, for example something like

mrs_tools merge --files rda1_off.nii.gz rda2_off.nii.gz --dim DIM_DYN --output merged --filename off
mrs_tools merge --files rda1_on.nii.gz rda2_on.nii.gz --dim DIM_DYN --output merged --filename on
mrs_tools merge --files merged/on.nii.gz merged/off.nii.gz --dim DIM_EDIT --newaxis --output merged --filename on_off

at any point you can see the shape of a file using

mrs_tools info file.nii.gz

or visualise it’s contents using

mrs_tools vis file.nii.gz [--display_dim DIM_EDIT]
1 Like
5

I’ve just emailed you to get further details regarding this and will post here once I’ve fixed the two issues with RDA files.

6

I’ve updated Gannet to now handle conjoining Siemens RDA files. The command syntax is slightly different than joining other data formats: see here for details.

I’ve also fixed the RDA header problem.