-
Notifications
You must be signed in to change notification settings - Fork 95
New issue
Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.
By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.
Already on GitHub? Sign in to your account
[DOC] Add information about using tedana with fMRIPrep v21.0.0 #847
Changes from all commits
8f1627c
766feb4
74791fe
3442f42
27e5342
8297654
File filter
Filter by extension
Conversations
Jump to
Diff view
Diff view
There are no files selected for viewing
Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -1,3 +1,4 @@ | ||
.DS_Store | ||
docs/generated/ | ||
.pytest_cache/ | ||
|
||
|
Original file line number | Diff line number | Diff line change |
---|---|---|
|
@@ -10,7 +10,26 @@ FAQ | |
[tedana] How do I use tedana with fMRIPrepped data? | ||
*************************************************** | ||
|
||
`fMRIPrep`_ outputs the preprocessed, optimally-combined fMRI data, rather than echo-wise data. | ||
fMRIPrep versions >= 21.0.0 | ||
=========================== | ||
|
||
Starting with version 21.0.0, `fMRIPrep`_ added the ``--me-output-echos`` argument, | ||
which outputs individual echoes after slice timing, motion correction, and distortion correction have been performed. | ||
These preprocessed echoes can be denoised with tedana, | ||
after which warps written out by fMRIPrep can be applied to transform the denoised data to standard space. | ||
|
||
As the fMRIPrep outputs become more formalized, | ||
it is possible to write functions that can select the appropriate derivative files and run tedana on them. | ||
Below is one example of such a function. | ||
|
||
.. raw:: html | ||
|
||
<script src="https://gist.github.com/jbdenniso/73ec8281229d584721563a41aba410cf.js"></script> | ||
|
||
fMRIPrep versions < 21.0.0 | ||
========================== | ||
|
||
Prior to version 21.0.0, `fMRIPrep`_ outputted the preprocessed, optimally-combined fMRI data, rather than echo-wise data. | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Technically, it could also output preprocessed, individual echos using the |
||
This means that you cannot use the standard fMRIPrep outputs with tedana for multi-echo denoising. | ||
|
||
However, as long as you still have access to fMRIPrep's working directory, | ||
|
@@ -24,18 +43,23 @@ Unfortunately, fMRIPrep's working directory structure is not stable across versi | |
so writing code to grab the relevant files from the working directory is a bit of a moving target. | ||
Nevertheless, we have some code (thanks to Julio Peraza) that works for version 20.2.1. | ||
|
||
.. warning:: | ||
We will try to keep the following gist up-to-date, but there is no guarantee that it will work for a given version. | ||
Use it with caution! | ||
|
||
If you do find that the gist isn't working for an fMRIPrep version >= 20.2.1, | ||
please comment on `Issue #717 <https://github.com/ME-ICA/tedana/issues/717>`_ (even if it's closed) | ||
and we will take a look at the problem. | ||
|
||
Comment on lines
-27
to
-34
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Given that fMRIPrep added an option to output individual echoes, we don't really need to keep the gist up to date. |
||
.. raw:: html | ||
|
||
<script src="https://gist.github.com/tsalo/83828e0c1e9009f3cbd82caed888afba.js"></script> | ||
|
||
Warping scanner-space fMRIPrep outputs to standard space | ||
======================================================== | ||
|
||
Here is a basic approach to normalizing scanner-space tedana-denoised data created from fMRIPrep outputs, | ||
using ANTS's antsApplyTransforms tool. | ||
The actual filenames of fMRIPrep derivatives depend on the filenames in the BIDS dataset | ||
(e.g., the name of the task, run numbers, etc.), | ||
but in this example we chose to use the simple example of "sub-01" and "task-rest". | ||
The standard space template in this example is "MNI152NLin2009cAsym", but will depend on fMRIPrep settings in practice. | ||
|
||
.. raw:: html | ||
|
||
<script src="https://gist.github.com/tsalo/f9f38e9aba901e99ddb720465bb5222b.js"></script> | ||
|
||
************************************ | ||
[tedana] ICA has failed to converge. | ||
|
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
I was getting the following when I built the docs locally:
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
It seems like either now work, so I'm fine with this as-is !