Hi, I am having some problems reconstructing my MRI data with Gadgetron. Here is a brief description of my data:
It is a set of dynamic data acquired in hybrid 3D k-space----phase-encoding in the slice direction (but 80% partial acquisition: 26 phase-encoding steps for 32 slices) and golden angle radial spokes in x-y plane.
As far as I understand, the built-in functionality of Gadgetron deals with 2D data as well as multi-slice data, but not this type.
So I am wondering what I can do to get it reconstructed using Gadgetron, please?
Thanks a lot!
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It is basically impossible to answer this question without more knowledge
about your data.
Do you acquire the same k-space lines in each of your slice phase encoding
steps?
If yes, then you can simply to a point by point iFFT along the slice
direction to and then send the data onto the 2D golden angle radial recon
slice by slice. You would need to write some code for those initial steps
and book keeping. Again, hard to say in general what to do since I don't
know your data layout.
If no, then you need to treat it as a 3D encoding space. There would be
some work to do to make that work and depending on the size of your problem
it may not be suitable for GPU processing which is what is currently done
in the golden angle recon.
Hi, I am having some problems reconstructing my MRI data with Gadgetron.
Here is a brief description of my data:
It is a set of dynamic data acquired in hybrid 3D
k-space----phase-encoding in the slice direction (but 80% partial
acquisition: 26 phase-encoding steps for 32 slices) and golden angle radial
spokes in x-y plane.
As far as I understand, the built-in functionality of Gadgetron deals with
2D data as well as multi-slice data, but not this type.
So I am wondering what I can do to get it reconstructed using Gadgetron,
please?
Hi, I appreciate your kind response. Yes, as you expected, we acquired the same radial spoke for all the 26 slice phase encodes, and then move to the next angular position. We tried to do what you have suggested: do some programming to first resolve all the slices and feed the data into Gadgetron. And the most convenient way for me to do that is using Matlab, so I resorted to the example Matlab code "test_create_dataset.m" under the ismrmrd/example/matlab directory, trying to use it as a template for writing my own code. Unfortunately, that example code doesn't seem to work. I am sure I have the newest ISMRMRD and have all the necessary libraries installed. So do you have any suggestions for this, please?
Thank you very much for your time.
Regards
Xia
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
As you can see in other threads on this forum, the Matlab components are an
undocumented, buggy part of the Gadgetron, which is still being developed.
I would not recommend that as a place to start right now.
Your best bet is to create a Gadget (in C++), which a) buffers the incoming
projections, b) when all slice-phase encoding steps have been completed
does an FFT along the slice direction, c) sends the profiles down the
stream. There is really no other way of doing this than just rolling up
your sleeves and programming it. It can probably be done in 50 lines or
less, but it may take you some time the first time around.
Before going down that path, I would experiment with the 2D golden angle
reconstructions first and see if they actually do what you would need them
too.
Hi, I appreciate your kind response. Yes, as you expected, we acquired the
same radial spoke for all the 26 slice phase encodes, and then move to the
next angular position. We tried to do what you have suggested: do some
programming to first resolve all the slices and feed the data into
Gadgetron. And the most convenient way for me to do that is using Matlab,
so I resorted to the example Matlab code "test_create_dataset.m" under the
ismrmrd/example/matlab directory, trying to use it as a template for
writing my own code. Unfortunately, that example code doesn't seem to work.
I am sure I have the newest ISMRMRD and have all the necessary libraries
installed. So do you have any suggestions for this, please?
Hi, I am having some problems reconstructing my MRI data with Gadgetron. Here is a brief description of my data:
It is a set of dynamic data acquired in hybrid 3D k-space----phase-encoding in the slice direction (but 80% partial acquisition: 26 phase-encoding steps for 32 slices) and golden angle radial spokes in x-y plane.
As far as I understand, the built-in functionality of Gadgetron deals with 2D data as well as multi-slice data, but not this type.
So I am wondering what I can do to get it reconstructed using Gadgetron, please?
Thanks a lot!
It is basically impossible to answer this question without more knowledge
about your data.
Do you acquire the same k-space lines in each of your slice phase encoding
steps?
If yes, then you can simply to a point by point iFFT along the slice
direction to and then send the data onto the 2D golden angle radial recon
slice by slice. You would need to write some code for those initial steps
and book keeping. Again, hard to say in general what to do since I don't
know your data layout.
If no, then you need to treat it as a 3D encoding space. There would be
some work to do to make that work and depending on the size of your problem
it may not be suitable for GPU processing which is what is currently done
in the golden angle recon.
Michael
On Sun, Feb 16, 2014 at 11:11 AM, Xia zxmri@users.sf.net wrote:
Last edit: Xia 2014-02-17
Last edit: Xia 2014-02-17
Dr. Hansen,
Hi, I appreciate your kind response. Yes, as you expected, we acquired the same radial spoke for all the 26 slice phase encodes, and then move to the next angular position. We tried to do what you have suggested: do some programming to first resolve all the slices and feed the data into Gadgetron. And the most convenient way for me to do that is using Matlab, so I resorted to the example Matlab code "test_create_dataset.m" under the ismrmrd/example/matlab directory, trying to use it as a template for writing my own code. Unfortunately, that example code doesn't seem to work. I am sure I have the newest ISMRMRD and have all the necessary libraries installed. So do you have any suggestions for this, please?
Thank you very much for your time.
Regards
Xia
As you can see in other threads on this forum, the Matlab components are an
undocumented, buggy part of the Gadgetron, which is still being developed.
I would not recommend that as a place to start right now.
Your best bet is to create a Gadget (in C++), which a) buffers the incoming
projections, b) when all slice-phase encoding steps have been completed
does an FFT along the slice direction, c) sends the profiles down the
stream. There is really no other way of doing this than just rolling up
your sleeves and programming it. It can probably be done in 50 lines or
less, but it may take you some time the first time around.
Before going down that path, I would experiment with the 2D golden angle
reconstructions first and see if they actually do what you would need them
too.
On Mon, Feb 17, 2014 at 11:52 AM, Xia zxmri@users.sf.net wrote:
Dr. Hansen,
I have found a way around this problem and successfully fed my data into Gadgetron, and the recon looks good.
Thanks again for your kind help!
Regards
Xia