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

Jump to bottom

NF: Output BOLD HMC transforms and reference volume #2860

Merged
merged 1 commit into from
Oct 12, 2022
Merged

NF: Output BOLD HMC transforms and reference volume #2860

merged 1 commit into from
Oct 12, 2022

Conversation

effigies
Copy link
Member

Closes #2803. The format is up for debate, but this is what we use internally, and it's pretty reasonable.

cc @Lestropie

@effigies effigies force-pushed the enh/motion_xforms branch 2 times, most recently from 5bfd31b to 1982dd8 Compare September 27, 2022 12:35
@effigies effigies self-assigned this Sep 27, 2022
@effigies
Copy link
Member Author

Here's an example (link probably won't work for long):
tmp/ds054/derivatives/fmriprep/sub-100185/func/sub-100185_task-machinegame_run-01_from-scanner_to-boldref_mode-image_xfm.txt

#Insight Transform File V1.0
#Transform 0
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 1 -5.63032e-05 9.56292e-05 5.64124e-05 0.999999 -0.00132235 -9.55647e-05 0.00132235 0.999999 -0.00951554 0.154872 -0.0395518
FixedParameters: 0 0 0
#Transform 1
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 1 0.000103325 0.000299206 -0.000103188 1 -0.000229664 -0.000299254 0.000229602 1 -0.0127712 0.0818696 0.0471371
FixedParameters: 0 0 0
#Transform 2
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 1 9.66473e-05 -0.000163583 -9.63369e-05 0.999998 0.00226405 0.000163766 -0.00226404 0.999998 -0.0114369 0.0454862 0.191359
FixedParameters: 0 0 0
#Transform 3
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 1 -1.0613e-05 1.80126e-05 1.0622e-05 1 -0.000249124 -1.80073e-05 0.000249124 1 -0.00918892 0.15731 -0.0512331
FixedParameters: 0 0 0
#Transform 4
Transform: MatrixOffsetTransformBase_double_3_3
Parameters: 0.999999 0.00030273 0.000642284 -0.000303562 0.999999 0.000647455 -0.000641891 -0.000647844 0.999999 -0.00834608 0.0187707 0.0370819
FixedParameters: 0 0 0

@effigies effigies mentioned this pull request Sep 29, 2022
Closed
@effigies effigies added this to the 22.1.0 milestone Oct 11, 2022
mgxd
mgxd approved these changes Oct 11, 2022
View reviewed changes
Copy link
Collaborator

@mgxd mgxd left a comment

Choose a reason for hiding this comment

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

LGTM

fmriprep/workflows/bold/base.py Show resolved Hide resolved
fmriprep/workflows/bold/outputs.py
@@ -220,6 +220,7 @@ def init_func_derivatives_wf(
't2star_std',
'bold2anat_xfm',
'anat2bold_xfm',
'hmc_xforms',
Copy link
Collaborator

Choose a reason for hiding this comment

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

And this one to the docstring inputs

Copy link
Member Author

Choose a reason for hiding this comment

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

This function doesn't have docstrings for input/output nodes.

@effigies effigies merged commit 7124ef2 into nipreps:master Oct 12, 2022
@effigies effigies deleted the enh/motion_xforms branch October 12, 2022 17:29
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers

@mgxd mgxd mgxd approved these changes

Assignees

@effigies effigies

Labels
None yet
Projects
Development
Status: Released
Milestone
22.1.0
Development

Successfully merging this pull request may close these issues.

Output motion transforms in BIDS Derivatives
2 participants
@effigies @mgxd