-
-
Notifications
You must be signed in to change notification settings - Fork 5
Problem using "resliceimg" #161
Comments
@evaalonsoortiz the link to the data brings me here: correct link: https://github.com/shimming-toolbox/data-testing/tree/master/realtime_zshimming_data |
trying to reproduce this issue, running into another error: Version of shimming-toolbox: 9081cda
|
@evaalonsoortiz could you please provide more information so i can reproduce this issue? |
link updated |
The paths need to be entered with single quotations around them: I am using the latest commit to master. Can you tell me how you obtain the version number, like you shared above? |
cd into the git repository and type:
or a more fancy look at the history:
I made these useful aliases in my bash_profile:
|
after using the single quotes as suggested in shimming-toolbox/shimming-toolbox#161 (comment), i ran into the following issue (still a different error message than the one reported in shimming-toolbox/shimming-toolbox#161 (comment)): Full output
@evaalonsoortiz did you go that far in the processing or does your error appear afterwards? |
@jcohenadad I believe you are getting that error because we only kept 10 field mapping volumes, whereas the original acquisition had 60 (and the dicom header states that there are 60 volumes). Perhaps we should go back to the example data and keep the 60 volumes. |
just checked, that ^ is why. the |
The realtime_zshimming.m script uses a time series of B0 maps to compute the static and dynamic shim gradients that are needed for z-shimming. If z-shimming is going to be done with a gradient echo scan, then realtime_zshimming.m requires a sample magnitude gradient echo scan so that the static and dynamic shim gradient images can be resampled to the resolution of the gradient echo scan.
"realtime_zshim.m" calls
resliceimg
here:https://github.com/shimming-toolbox/shimming-toolbox/blob/9081cdac6701d7df74c5db109c205655be10d54e/example/realtime_zshim.m#L310
Instead of doing realtime z-shimming with a gradient echo scan, I am attempting to do it with an EPI scan. This means that realtime_zshimming.m will use an EPI scan to resample the static and dynamic shim gradient maps to the resolution of EPI scan. When trying this, I run into the following error:
There is sample data to test this out here. The realtime_zshim.m script can be called using
realtime_zshim('phantom')
in the folder containing the sample data. You will then be prompted to enter the paths of the B0 maps and the EPI (or GRE) images.The text was updated successfully, but these errors were encountered: