Thank you for your reply and comments.First, I realized now that I wrote the example for the index and acqparams information opposite way.Thank you for correcting it, and when I run the pre-processing, I used it in the correct way.
Regarding the Question 1 comment: the TotalReadoutTime '0.55',1. The data which I used, some of it has TotalReadoutTime, but some of it doesn't have.
2. I asked how I can set the value to the person, one of whom is in charge of those data, and I could receive the answer as below.'Eddy can be run without topup, but it will ask for the echo spacing. I use 0.55 ms'.(I couldn't use the topup, because I only have one phase of b=0.)→I thought this answer means that I can use 0.55 for the TotalReadoutTime value.
When I got the error message, I thought the message seems to occur due to the 'acqparam.txt' value.I found some people use 0.05 for the value TotalReadoutTime. However, when I use 0.05, I also get the same error message.
Therefore, may I ask you for some advice to solve the issue please?
Thank you in advance for your comments.I hope everything is going well with you.
Sincerely,DaWoon
Dear DaWoon,
For the acqparams.txt, I made it by input '1' with the length which is the same size as volumes.(e.g. 5 volumes → 1 1 1 1 1)what you are describing here is what should be in the --index file, _not_ in the --acqp file.
In addition, I write index.txt as '0 1 0 TotalReadoutTime' or '0 1 0 0.55'.
And this is what should be in the --acqp file.
However, the total readout time that you have given here is completely unrealistic. If that was true your images would be so distorted they wouldn't even look like images. And eddy does a sanity check for that. How did you arrive at this number?
Question 2. [semi-solved]
Below is the error message.EDDY::: ECScanManager::GetShellIndicies: Data not shelled
EDDY::: ECScanClasses.cpp::: std::vector<std::vector<unsigned int> > EDDY::ECScanManager::GetShellIndicies(std::vector<double>&) const: Exception thrown
EDDY::: Eddy failed with message EDDY::: ECScanClasses.cpp::: EDDY::ECScanManager::ECScanManager(const string&, const string&, const string&, const string&, const string&, const string&, const string&, const string&, EDDY::ECModel, EDDY::ECModel, const std::vector<unsigned int>&, const EDDY::PolationPara&, EDDY::MultiBandGroups, bool): Exception thrown
It was solved by adding the '--data_is_shelled' option in the upper (a) part.
However, can I use this option for whole data, including which data runs well without that option?You can use this option, but it should _only_ be used if you know for certain data is shelled. I.e. it should not be used to run eddy on DSI data, because it would not give good results on that.
Jesper
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