Fails conversion with tonii_all

[mschneider1711]

Describe the bug
A clear and concise description of what the bug is.
When I want to convert multiple datasets with tonii_all at the same time I get a bug that the input folder is not valid.

When I comment out the section where it checks if the parent folder is a pv_dataset it works and all my files are converted into nifti.
My folder structur is:

Expected behavior
In my case the BidsData folder should not be recognized as a pv_dataset and therefore the script should not stop at this point.

Desktop (please complete the following information):

• Windows 11
• Version v.0.3.10

@Aswendt-Lab
@arefks
@maswendt

[gdevenyi]

Please share the complete command you are using.

[mschneider1711]

That's the command I'm using:

[gdevenyi]

And what are the contents of one of the subfolders of BidsData?

[mschneider1711]

It is the raw dataset.

[gdevenyi]

Ok, the error is as expected. The tonii_all command is intended to be run on a single dataset, whereas you are running it on multiple datasets.

The error could be better in terms of what it says, since it wrongly indicates you're running on a single scan.

I think the solution here is an optional flag to tonii_all --recursive which will recurse down directories.

[mschneider1711]

Unfortunately I get the same error when using it on a single dataset:

[dvm-shlee]

@mschneider1711, apologies for the delayed response. Have you managed to resolve the issue? If not, could you please share the contents of the /Data folder located under /BidsData?

It seems there might be a misunderstanding causing the brkraw tonii_all command to treat BidsData as a single raw data set, whereas your initial method should have worked as expected. I am actively working on addressing issues within the BrkRaw package and expect to have enhancements ready by mid-May. If you're still encountering problems, I can assist you in testing with the new module, which should present fewer issues than the current version. Please consider that the complete code will be ready by May 15th.

[MrImaging]

I experienced this issue as well and could resolve it/work around it by zipping the raw data sets/folders, which then allowed me to apply tonii_all to multiple subjects and sessions simultaneuosly