Skip to content
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.

Sign up for GitHub

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

Add metadata for motion parameters #3245

Merged
merged 7 commits into from
Mar 4, 2024
Merged

Add metadata for motion parameters #3245

Changes from 3 commits
Commits
Show all changes
7 commits
Select commit Hold shift + click to select a range
6ce9e06
Add metadata for base motion parameters.
tsalo Mar 2, 2024
0100609
Update the metadata.
tsalo Mar 2, 2024
bc6be11
Switch from double-quotes to single-quotes.
tsalo Mar 2, 2024
0121be2
Fix motion regressor descriptions.
tsalo Mar 2, 2024
d30c1b1
Update fmriprep/workflows/bold/confounds.py
tsalo Mar 2, 2024
64d1b41
Merge remote-tracking branch 'upstream/master' into motion-metadata
tsalo Mar 2, 2024
83f77a1
Merge branch 'motion-metadata' of https://github.com/tsalo/fmriprep i…
tsalo Mar 2, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
14 changes: 13 additions & 1 deletion fmriprep/workflows/bold/confounds.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -412,10 +412,22 @@ def init_bold_confs_wf(
name='crowncc_metadata_fmt',
)

# Combine all confounds metadata
mrg_conf_metadata = pe.Node(
niu.Merge(3), name='merge_confound_metadata', run_without_submitting=True
niu.Merge(4), name='merge_confound_metadata', run_without_submitting=True
)
# Tissue mean time series
mrg_conf_metadata.inputs.in3 = {label: {'Method': 'Mean'} for label in signals_class_labels}
# Movement parameters
mrg_conf_metadata.inputs.in4 = {
'trans_x': {'Description': 'Translation Along X Axis', 'Units': 'mm'},
'trans_y': {'Description': 'Translation Along Y Axis', 'Units': 'mm'},
'trans_z': {'Description': 'Translation Along Z Axis', 'Units': 'mm'},
'rot_x': {'Description': 'Rotation Along X Axis', 'Units': 'rad'},
'rot_y': {'Description': 'Rotation Along Y Axis', 'Units': 'rad'},
'rot_z': {'Description': 'Rotation Along Z Axis', 'Units': 'rad'},
Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Should be rotation "about". And could we indicate the x axis is left-right, and so on?

Copy link
Collaborator Author

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Absolutely can do. Just to make sure, the motion parameters don't depend on the phase encoding direction? Meaning they don't directly map onto i, j, and k at this point?

Copy link
Member

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Hmmm, would be good to check.

'framewise_displacement': {'Units': 'mm / TR'},
tsalo marked this conversation as resolved.
Show resolved Hide resolved
}
mrg_conf_metadata2 = pe.Node(
DictMerge(), name='merge_confound_metadata2', run_without_submitting=True
)
Expand Down