Comments (7)
It's not exactly an error. Is the conversion failing? and what is mMR?
from siemens_to_ismrmrd.
Thank you for your prompt reply!
Is the conversion failing?
This is a good question. We don't have the means to reconstruct this dataset accurately.
As far as I understand, 3D spiral with Gadgetron is not supported yet.
However, running siemens_to_ismrmrd -f XXX.dat -z 2 -X
a colleague got some promising results with some custom reconstruction.
Without the flags -z 2 -X, the executable does not create an mrd
file.
and what is mMR?
It is this scanner here
from siemens_to_ismrmrd.
Not totally sure how to help here, -z 2
means the second measurement in the dat file. The first one is probably dependencies. -X
just means to dump some debug information, so I am guessing it is the -z 2
that "makes it work" for you and you get an ISMRMRD file. If you can reconstruct (with some reconstruction), then that would seem to be OK, or am I missing something?
from siemens_to_ismrmrd.
In the images, we get some strong artifacts (primarily truncation for now), and I am trying to figure out whether this could have something to do with the warning.
from siemens_to_ismrmrd.
Trying to debug this from reconstructed images is probably going to be tough. I would start by validating that you have the right number of readouts (acquisitions) in the dataset and that each of the readouts have the correct number of samples. I would also check the XML header to see if it it has the expected information. If that checks out, it is probably not a conversion problem.
from siemens_to_ismrmrd.
Hi all,
I am picking up this thread. I have made a lot of progress and practically I am able to reconstruct most of the data I acquire.
However, in some datasets, not all of them this flag gets triggered
if ((scanhead.aulEvalInfoMask[0] & (1ULL << 10)))
ismrmrd_acq.setFlag(
ISMRMRD::ISMRMRD_ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA);
I know that the data are part of the k-space, so some times this bit flags inaccurately as correction data.
Any ideas?
from siemens_to_ismrmrd.
I believe this could be a misnomer of the flag:
If I understand correctly, scanhead.aulEvalInfoMask[0][10]
signifies that the data needs a raw data correction, i.e. acquisitions with this flag enabled should be multiplied by a factor. The factor can be found in the raw file as dRawDataCorrectionFactorRe
/ dRawDataCorrectionFactorIm
for each coil.
I think it does not mean that this data is actual correction data and can be ignored.
Not sure if this is a bug in the converter or just unfortunate naming, either way it is a bit non-obvious how to interpret ISMRMRD_ACQ_IS_SURFACECOILCORRECTIONSCAN_DATA
and could maybe be documented somewhere.
Maybe somebody with more knowledge about the Siemens data and the ISMRMRD specification can chime in?
from siemens_to_ismrmrd.
Related Issues (20)
- tell CMake what version of ISMRMRD is required HOT 3
- Converter trajectoryDescription: Schemas validity error for XA30, but not VE11C HOT 11
- Required Boost version is missing HOT 5
- v1.2.3 not present on conda package repository HOT 2
- Problems with extracting data HOT 6
- Unsaved profiles flags multi-echo GRE 7T HOT 7
- Privacy issue HOT 2
- Conversion problem with Magnetom Sola data HOT 4
- Noise bandwidth is incorrect in Numaris/X
- error while loading shared libraries: libismrmrd.so.1.13 HOT 12
- Mis-use of userindices HOT 3
- Unknown CMake command "set_and_check". HOT 5
- Unable to convert the raw data to ISMRMRD format due to "invalid_argument" HOT 1
- Failed to find YAPS.iNoOfFourierLines array HOT 1
- MR XA50 "terminate called after throwing an instance of 'std::runtime_error' what(): Malformed file" HOT 4
- Installation instructions missing dependency [+ possible step] HOT 1
- Output processed.xml in debug even when XML is not valid
- Parameter map for raw data from Cima.X (syngo MR XA61) HOT 1
- Pulseq acquisitions fail to convert when '3D' is selected HOT 6
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