Comments (10)
@hansenms any reason this issue was closed without fixing
IsmrmrdParameterMap_Siemens_EPI_FLASHREF.xsl and IsmrmrdParameterMap_Siemens_T1Mapping_SASHA.xsl?
from siemens_to_ismrmrd.
It has been open since 2017 with no repro and no suggested fix. If this is an issue we need a proper repro. Like an example dataset and a clear description of what your expected behavior is and what exactly you are seeing. Ideally there would be a PR to fix it.
So I mostly closed it because I figured if it had been sitting since 2017 without a PR it was probably no longer relevant. I would propose a PR instead of an issue if you have a fix.
from siemens_to_ismrmrd.
Understood. Can I suggest you keep this issue closed but assign the label wontfix
. I did provide a link to a repository that provides sample images with different partial Fourier settings. However, it is completely understandable that addressing this is outside of the remit of the current developers. Both dcm2niix and GDCM provide correct solutions for any future users that need to accurately determine pF.
from siemens_to_ismrmrd.
I wouldn’t say it’s a won’t fix. Somebody just needs to take it on. There is a tendency that a lot of issues get opened with an expectation that some army of devs jump on and solve it. The reality is that you are probably in the best position to fix this and would have the test cases etc. Also in this case, the PR would probably be less text than this discussion. So if somebody would like a style sheet changes, let’s just get a PR.
from siemens_to_ismrmrd.
Actually, I am reopening this. It is not 100% clear these values are to be interpreted the same for all sequences and it may be intentional that they are the way that they are. However, we need to have a few more eyes on it. So I will put up a PR (#89) and have somebody else take a look at it.
In the future, it is a huge help if you just put up a PR for this sort of thing. Much quicker to move it through. Issues that require somebody else (who is not focused on it and has no tests cases) tend to just sit there.
from siemens_to_ismrmrd.
@hansenms I do believe that ucPhasePartialFourier
is described similarly across all Siemens sequences - I have never heard of any errors from dcm2niix users. However, I would be happy to acquire some public validation datasets on our VE11C Siemens Prisma if someone can send me a sample of the EPI_FLASHREF
or T1Mapping_SASHA
DICOMs that I can Phoenix onto our system (send to the email listed in my avatar). I do host a number of public DICOM validation datasets dcm_qa* that might be useful for testing the siemens_to_ismrmrd
project. I have also sent an email to our Siemens Research Collaboration Manager to verify that ucPhasePartialFourier
has a single definition across all sequences.
from siemens_to_ismrmrd.
Let's see if @kspaceKelvin can get us the information. It would not be the first time that a parameter is interpreted differently for different sequences. For phase resolution some sequences round up, others down, etc. It happens. That is why we have style sheets so that these things can be adjusted. The PR is up and let's see what Kelvin says and take it from there,
from siemens_to_ismrmrd.
@hansenms it would be great to have sample images that demonstrate the need for various style sheets. If we can isolate the situations, we can usually get support from the manufacturer engineers to develop a formula without a style sheet. This sounds a lot like the Round_factor
that GE uses which was completely mysterious until the GE engineers described the formula they use. Even if style sheets are required, it would be nice to demonstrate these edge cases for the community, helping other tools like dicm2nii and dcm2niix.
from siemens_to_ismrmrd.
Yeah, images are not really what we are looking for here, since we care about the interpretation of the raw data, which may yield different images depending on the reconstruction.
In terms of getting to a formula, then I don’t think it’s possible or even desirable in general. There are some classes of sequences that tend to yield similar interpretation of the parameters so we can probably cover most sequences with a few style sheets but there will be variations. Moreover, custom research sequences may have a completely different interpretation which may be a total hack but having the stylesheets allows users to accommodate that and still get usable reconstructions. I don’t see any specific advantage in trying compile in a formulate. The stylesheets are a good trade off between between being prescriptive and flexibility.
That said, there are repetitive sections in stylesheets and some kind of include function would be nice so we don’t have to edit the same thing in many places.
And example datasets are of course great to illustrate different cases, so we could do more there. But critically this should not be images but raw datasets.
On GE they are in much much worse shape when it comes to getting close to a formula. And most GE raw datasets cannot be interpreted without actually “knowing” what the sequence did. There is nothing in the dataset to even apply a stylesheets to. That’s why the GE converter also requires a sequence specific compiled component to interpret the profile ordering. Rounding is the least of our worries there ;)
from siemens_to_ismrmrd.
Heh, my bad for not updating all of the stylesheets when I changed it in #18 . This interpretation is correct for all sequences as of the current software version.
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
- Error converting Spiral from mMR to ismrmrd HOT 7
- Parameter map for raw data from Cima.X (syngo MR XA61) HOT 1
- Pulseq acquisitions fail to convert when '3D' is selected HOT 6
Recommend Projects
-
React
A declarative, efficient, and flexible JavaScript library for building user interfaces.
-
Vue.js
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
-
Typescript
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
-
TensorFlow
An Open Source Machine Learning Framework for Everyone
-
Django
The Web framework for perfectionists with deadlines.
-
Laravel
A PHP framework for web artisans
-
D3
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
-
Recommend Topics
-
javascript
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
-
web
Some thing interesting about web. New door for the world.
-
server
A server is a program made to process requests and deliver data to clients.
-
Machine learning
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
-
Visualization
Some thing interesting about visualization, use data art
-
Game
Some thing interesting about game, make everyone happy.
Recommend Org
-
Facebook
We are working to build community through open source technology. NB: members must have two-factor auth.
-
Microsoft
Open source projects and samples from Microsoft.
-
Google
Google ❤️ Open Source for everyone.
-
Alibaba
Alibaba Open Source for everyone
-
D3
Data-Driven Documents codes.
-
Tencent
China tencent open source team.
from siemens_to_ismrmrd.