*+ WARNING: If you are performing spatial transformations on an oblique dset

[worgwis]

I run multi-echo on 7T The scanner output was 800 dicoms for 4 TEs (9.5 24.71 39.92 55.13), I sorted them into 4 folders and use dcm2niigui ('compressed FSL (4D NiftI')

I get an error when using meica.py *+ WARNING: If you are performing spatial transformations on an oblique dset, or viewing/combining it with volumes of differing obliquity, you should consider running: 3dWarp -deoblique

I run: 3dWarp -deoblique input.nii.gz (to each TE) and got .BRIK and .HEAD files... what should i do?

[dowdlelt]

Hi taliwe25

Is there a particular reason you are trying to use meica rather than tedana? This repository is considered outdated and is no longer maintained. Development has continued on tedana, the core multiecho/ICA processing code.

You can clone the repository and use it in a somewhat similar fashion. See here for the tedana code, https://github.com/ME-ICA/tedana and here https://tedana.readthedocs.io/en/latest/ for the tedana docs/installation guidelines etc.

The idea is that you would handle preprocessing of the echoes, and then pass the data through to tedana for optimal combination and denoising. This is contrast to the previous usage of MEICA, which performed a number of steps for you. If you would prefer to have the processing done in AFNI, as it was for MEICA, example 12 (and a few others) in the afni_proc.py help may be useful: https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html

In anycase, you do not need to run 3dWarp -deoblique, that will be handled by afni_proc and that error can be ignored in most cases.

Let me know if this makes sense. If you run into some problems, check the tedana issues or neurostars.org for the tedana flag - someone may have solved that problem previously.

[emdupre]

Thanks for reporting, @taliwe25 ! I'm a strong +1 on everything @dowdlelt outlined above.

I'm going to archive this repository: at this point, I think having it open for conversation is causing more confusion than anything else. This means that you'll no longer be able to post in this issue. To continue the conversation, I'd recommend moving to NeuroStars, as @dowdlelt outlined above.