registration assist does not read both functional scans

[amitch3]

I hope i can explain this issue accurately.

When using the --registration-assist flag for contrast enhanced (ce) functional images, the MOVING and REFERENCE files are incorrectly read into the appropriate space. essentially, from what i understand, when this flag is active the pipeline tries to register the normal bold scan (task-rest) to itself.

It appears to be doing this because the script is only looking for the phrase "task-rest" and once it finds it, it stops. Instead, it needs to continue and include more of the name to enable the pipeline to tell the difference. In the images below, the first one details the submission command and allows you to orient yourself. The latter describes where both the regular bold and contrast enhanced are using the same reference image.

[amitch3]

after additional troubleshooting, using this flag causes terminal errors within FMRIVolume.