Skip to content

New EPI dewarping workflow, in a similar manner to eddy_current correction #525

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
Merged
merged 2 commits into from
Mar 4, 2013
Merged

New EPI dewarping workflow, in a similar manner to eddy_current correction #525

merged 2 commits into from
Mar 4, 2013

Conversation

oesteban
Copy link
Contributor

This new feature implements the EPI dewarping methodology from epidewarp.fsl,
as a workflow and including some enhancements allowing:

  • Use for dMRI
  • Optional registration
  • New EPI parameters support (parallel imaging, reverse encoding)

Additionally, some improvements on the FSL FUGUE's API have been included:

  • Added --saveshift argument support
  • Added --warp argument support
  • Improved the output listing methods for coherence

@oesteban
New EPI dewarping using a workflow
cdf352e 
This new feature implements the EPI dewarping methodology from epidewarp.fsl,
as a workflow and including some enhancements allowing:
  * Use for dMRI
  * Optional registration
  * New EPI parameters support (parallel imaging, reverse encoding)

Additionally, some improvements on the FSL FUGUE's API have been included:
  * Added --saveshift argument support
  * Added --warp argument support
  * Improved the output listing methods for coherence
oesteban
oesteban reviewed Feb 27, 2013
View reviewed changes
nipype/interfaces/fsl/preprocess.py
@@ -1174,6 +1187,17 @@ def __init__(self, **kwargs):
super(FUGUE, self).__init__(**kwargs)
warn('This interface has not been fully tested. Please report any failures.')

def _parse_inputs(self, skip=None):
Copy link
Contributor Author

Choose a reason for hiding this comment

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

FUGUE's api changed to be more consistent with the features of this tool

Copy link
Member

Choose a reason for hiding this comment

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

Does this break backward compatibility with FSL 4.1?

Copy link
Contributor Author

Choose a reason for hiding this comment

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

No :)

@chrisgorgo
Copy link
Member

This looks excellent - thanks for the contribution. Could you please add an information to the changelog as well? Thanks!

@oesteban
Copy link
Contributor Author

(yes), but you mean the root/CHANGES file?

@chrisgorgo
Copy link
Member

yes - thanks!

@oesteban
New EPI dewarp workflow (#525)
a9a8f19 
  * Removed useless comment
  * Changelog updated
chrisgorgo added a commit that referenced this pull request Mar 4, 2013
@chrisgorgo
Merge pull request #525 from oesteban/master
68d71d8 
New EPI dewarping workflow, in a similar manner to eddy_current correction
@chrisgorgo chrisgorgo merged commit 68d71d8 into nipy:master Mar 4, 2013
@oesteban oesteban mentioned this pull request Mar 6, 2013
Merged
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni/resample
2a58098 
* master: (42 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni/to3d
784ab78 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into afni_interfaces
2d2809d 
* master:
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into connect_func
b812aea 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into enh/dcmstack
88fd4a2 
* master: (32 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into enh/vbm
1ccd02d 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into fsl_model
0328b0c 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nipy/trim
a54558f 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nipype_additions
3c8119f 
* master:
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into nitime
44b6585 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into spm_interfaces
9e5feaa 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Mar 27, 2013
Merge branch 'master' into ICC
30b6b0a 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 5, 2013
Merge branch 'master' into nipy/slice_motion
c60c4b9 
* master: (28 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 17, 2013
Merge branch 'master' into lif_fmri
a5fdf1c 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Apr 17, 2013
Merge branch 'master' into spm/gzip
a13768c 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
bpinsard pushed a commit to bpinsard/nipype that referenced this pull request Sep 11, 2013
Merge branch 'master' into mri_convert
baac8cb 
* master: (47 commits)
  fixed applymask output
  fixed test
  Fixed some details for the PR nipy#530
  Removed accidentally added files (nipy#530)
  Updated changelog
  Updated dMRI and fMRI pre-processing
  Added motion correction pipeline
  Modified FSL FLIRT interface to provide log support
  Polished code
  buildtemplateparallel.sh - issue with input files
  Update legacy.py - buildtemplateparallel.sh
  Minor fixes
  Added MBIS to sub-package configuration list
  Standardized import to add all utilities at once
  First implementation for MBIS
  New EPI dewarp workflow (nipy#525)
  New EPI dewarping using a workflow
  api: force users to explicitly define whether to sort files
  BF: Fix SplitNifti to generate unique filenames for outputs.
  added mask input for bias field correction
  ...
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
2 participants
@oesteban @chrisgorgo