Comments (7)
There is not a 1:1 correspondence between flags in Siemens MDH header and ISMRMRD Acquisition flags, so I would not expect all flags to just be reproduced. You may have to modify the code the make sure the specific flags you want are transferred.
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Thank you for your quick response. I know there is no correspondence between the Siemens MDH flags and the ISMRMRD Acquisition flags. I am only considering the ISMRMRD flags. I would expect 31 flags to be saved in the .h5 file because this is the number of flags that are converted from Siemens MDH to ISMRMRD. Indeed, when I print the flags after the conversion, from the siemens_to_ismrmrd code (e.g., within the function ismrmrd_append_acquisition) I get 31 values. However, when I read the flags from the converted .h5 file, I only get the first 25 values. As you say, I could move the relevant flags in the first 25 bits, but I feel like this is not an optimal solution as other researchers may encounter the same problem.
This only happens for 7T data acquired with the GRE sequence. I have not tested other sequences, but for data collected at 3T with the same sequence, all 31 ISMRMRD flags are saved and available to be read from the .h5 file.
from siemens_to_ismrmrd.
I am very puzzled by this. Especially your last statement. At first, I thought there might be a bug in the converter or more specifically the ISMRMRD library that means that the last flags are not written to the file, but you say it works with some files and not with others, which is surprising. Would it be possible for you to post some more details and possibly data to reproduce this problem?
from siemens_to_ismrmrd.
I can share some phantom data acquired at 3T and 7T with the multi-echo GRE sequence. The 3T data are under-sampled, the 7T data are not, but the outcome is the same with 7T under sampled data. Let me know if you need more details in order to reproduce the problem.
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@xueh2 or @kspaceKelvin would you guys have any thoughts here.
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What is the software version for the data? VE or NX?
from siemens_to_ismrmrd.
@xueh2 the software version is VE for both acquisitions.
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Related Issues (20)
- Privacy issue HOT 2
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- error while loading shared libraries: libismrmrd.so.1.13 HOT 12
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- Unknown CMake command "set_and_check". HOT 5
- Unable to convert the raw data to ISMRMRD format due to "invalid_argument" HOT 1
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- 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
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- Error converting Spiral from mMR to ismrmrd HOT 7
- Parameter map for raw data from Cima.X (syngo MR XA61) HOT 1
- linking errors with hdf5
- 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
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