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Finalize afni_proc.py
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#29
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In addition to the section you copied from https://afni.nimh.nih.gov/pub/dist/doc/program_help/afni_proc.py.html examples 12-13 list multiple ways to use multi-echo with AFNI. The one you copied includes
If any of those options are used, it will run whichever version of
Last time I asked @mrneont and @afni-rickr they had no plans to have afni_proc natively use something similar to BIDS-derivatives filenaming, but |
My goal would actually be to run tedana separately, since these datasets are meant to act as inputs to tedana. Can afni_proc be used to produce minimally-preprocessed echo-wise outputs?
That's a great idea! I'll try that. |
If you use you the example you copied with |
@handwerkerd sorry for the noise. I don't know where I copied the incorrect parameters from. As far as a good repo for a template script goes, what about the Multi-echo masking test dataset (https://openneuro.org/datasets/ds002156)? There's only one subject, so it's small. The inputs can be:
The echo times are 15.1, 28.7, 42.3, and 55.9. I'm hoping that afni_proc can be used to produce (1) minimally-preprocessed echo-wise data to run tedana on, (2) a brain mask in the echo-wise images' space for tedana, and (3) optimally-combined data in standard space, which I could denoise using the tedana results. What do you think? |
Howdy- We actually do have a mapping of For multiecho FMRI data, we do have a fair number of
https://afni.nimh.nih.gov/pub/dist/OHBM2022/OHBM2022_tayloretal_apmulti.pdf @tsalo : it sounds like you want just the datasets output by using OC or tedana, then? Or with further regression processing? Are the pbcombine datasets what you would like, at present? --pt |
@tsalo Do you want the data aligned to a template space or in native space? If you want a template, which one? |
@mrneont that's awesome! I mainly want these AFNI derivatives to be useful for testing tedana, so the primary output I'm interested in is minimally-preprocessed individual echoes, along with some way to either transform outputs from running tedana separately on those echoes to standard space or optimally combined data in standard space that can be denoised using the results from running tedana separately. I'd love to have regressors that could be used for regression (e.g., motion parameters), but not denoised data. @handwerkerd if possible, I'd love to have the echo-wise outputs in native space (per our recommendations in the tedana docs) and optimally combined outputs in standard space. Maybe MNI152NLin6Asym, since that's the one I'll use for fMRIPrep? |
When afni_proc aligns to a template it does a single spatial transformation for both motion correction and alignment. (Probably time to revisit that recommendation ME-ICA/tedana#990 ). Do get what you want, I can write one afni_proc with and one without spatial alignment, or I can just run with spatial alignment and use a stand-along AFNI command to create volumes for each echo that aren't aligned to the template. AFNI includes a bunch of MNI templates, but I'm not sure which one matches MNI152NLin6Asym. Can you point me to the template volumes fMRIPrep uses so I can make sure to align to the exact same one? |
That would be great, thank you!
fMRIPrep grabs its templates from templateflow (https://www.templateflow.org/browse/). The template is under the |
AFNI does not need to have a template in the distribution to use it for template alignment. If there is one you like, just download and give it to afni_proc.py with the -tlrc_base option.
Yes, you can give afni_proc.py the echoes and just do the steps prior to 'combine', but really, it does not hurt to add 'combine' and 'regress' blocks. That would lead to a much more detailed QC report, and it won't change the datasets that you would want to use without those blocks. The cost is just extra disk space. But whatever you prefer is fine.
…-rick
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Subject: [EXTERNAL] Re: [ME-ICA/open-multi-echo-data] Finalize `afni_proc.py` settings (Issue #29)
Do get what you want, I can write one afni_proc with and one without spatial alignment, or I can just run with spatial alignment and use a stand-along AFNI command to create volumes for each echo that aren't aligned to the template.
That would be great, thank you!
AFNI includes a bunch of MNI templates, but I'm not sure which one matches MNI152NLin6Asym. Can you point me to the template volumes fMRIPrep uses so I can make sure to align to the exact same one?
fMRIPrep grabs its templates from templateflow (https://www.templateflow.org/browse/). The template is under the tpl-MNI152NLin6Asym folder. It's the file tpl-MNI152NLin6Asym_res-02_T1w.nii.gz.
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Here is a sample script for the above dataset. I have a version that runs
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Hi @handwerkerd. To get the EPI into standard space (without the extra resampling at the end), use: |
Hi @handwerkerd. The script worked, at least at a quick glance. I did use the blocks from above |
Thanks so much @afni-rickr @handwerkerd @mrneont! Our server is down at the moment, but I will try the updated command on one of the example datasets soon. |
@handwerkerd do you have any recommendations for running
afni_proc.py
on multi-echo data? Is there a way to ensure that the outputs are roughly similar to BIDS format?Here's a copy from the help (feel free to edit as you wish):
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