CSD always runs when multishell is set to TRUE, looking for file never generated

[njhunsak]

I'm trying to use the option 'computeCSD' and my data are multishell.

afq.params.track.multishell = true;
afq = AFQ_Create('sub_dirs', sub_dirs, 'sub_group', sub_group, 'showfigs', false, 'computeCSD', 1, 'normalization', 'ants');

I'm having issues with these options. Based on the code in AFQ_Create with the options I've included, this is the command that runs:

https://github.com/yeatmanlab/AFQ/blob/dd6c4789e5060e9300d2b925e502237dc4fbb93a/functions/AFQ_Create.m#L334-L340

That code creates a list of files:

https://github.com/yeatmanlab/AFQ/blob/dd6c4789e5060e9300d2b925e502237dc4fbb93a/utilities/AFQ_mrtrixInit.m#L116

Going to that script there's several files listed for CSD, but here's the file giving me issues:

https://github.com/yeatmanlab/AFQ/blob/dd6c4789e5060e9300d2b925e502237dc4fbb93a/utilities/AFQ_mrtrix_build_files.m#L37

Once you have the files listed, there's another program to check which mrtrix processes have been computed:

https://github.com/yeatmanlab/AFQ/blob/a42e1577772d7effa591b39c26acbabcdb69b32c/utilities/AFQ_mrtrixInit.m#L119

And here's the problem I'm having, the scripts are looking for the CSD file. However, that file is only created if multishell==0

https://github.com/yeatmanlab/AFQ/blob/a42e1577772d7effa591b39c26acbabcdb69b32c/utilities/AFQ_mrtrixInit.m#L231-L243

Since I'm using multishell, that CSD file is never created, so every time I run the AFQ_Create command, it always says CSD needs to be run.

It seems like somewhere when generating file names and checking those names to determine what mrtrix processes need to be run, there needs to be different criteria if multishell is set?

---

Also I had to change -tempdir to -scratch based on my version of mrTrix:

https://github.com/yeatmanlab/AFQ/blob/dd6c4789e5060e9300d2b925e502237dc4fbb93a/utilities/AFQ_mrtrix_5ttgen.m#L33

https://github.com/yeatmanlab/AFQ/blob/dd6c4789e5060e9300d2b925e502237dc4fbb93a/utilities/AFQ_mrtrix_5ttgen.m#L39