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

ENH: Restore resampling to T1w target #3116

Merged
merged 19 commits into from
Oct 26, 2023
Merged

ENH: Restore resampling to T1w target #3116

Changes from 1 commit
Commits
Show all changes
19 commits
Select commit Hold shift + click to select a range
9778661
ENH: Check for bold length before building workflow
effigies Oct 15, 2023
c67df4a
RF: Delete pieces already rewritten
effigies Oct 15, 2023
c4799a6
ENH: Add generic resampling workflow, use for anatomical
effigies Oct 16, 2023
9864b53
ENH: Add interpolation parameters to resampling interface
effigies Oct 17, 2023
8199d46
STY: Black
effigies Oct 17, 2023
41bc5f2
RF: Rename functions to match usage
effigies Oct 17, 2023
ded0a73
ENH: Add general volumetric datasink workflow
effigies Oct 17, 2023
c094f00
ENH: Hook up anatomical derivatives workflow
effigies Oct 18, 2023
7cc25d5
FIX: Names, connections, metadata
effigies Oct 18, 2023
ad3f392
FIX volumetric
effigies Oct 23, 2023
cac0b79
FIX: fmapreg_xfm -> boldref2fmap_xfm
effigies Oct 23, 2023
143a41f
FIX: Connect target_ref_file in volumetric resample workflow
effigies Oct 23, 2023
333a8fe
RF: Move coordinate copies into threads to delay allocation
effigies Oct 23, 2023
d2a3d95
FIX: Add sampling reference
effigies Oct 23, 2023
cf92a48
ENH: Construct resampled data array in F order
effigies Oct 23, 2023
83b8306
LOG: Move logging into init_bold_wf
effigies Oct 18, 2023
9bcfdac
RF: Remove old t1 workflow
effigies Oct 18, 2023
26d141f
RF: Move resampling to "full" section
effigies Oct 19, 2023
0d09cc0
Apply suggestions from code review
effigies Oct 26, 2023
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
Prev Previous commit
Next Next commit
STY: Black
  • Loading branch information
@effigies
effigies committed Oct 17, 2023
commit 8199d4633244615332369181f9ed5dfc5c266468
16 changes: 12 additions & 4 deletions fmriprep/interfaces/resampling.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,9 @@ class ResampleSeriesInputSpec(TraitedSpec):
in_file = File(exists=True, mandatory=True, desc="3D or 4D image file to resample")
ref_file = File(exists=True, mandatory=True, desc="File to resample in_file to")
transforms = InputMultiObject(
File(exists=True), mandatory=True, desc="Transform files, from in_file to ref_file (image mode)"
File(exists=True),
mandatory=True,
desc="Transform files, from in_file to ref_file (image mode)",
)
inverse = InputMultiObject(
traits.Bool,
Expand Down Expand Up @@ -120,10 +122,16 @@ class ReconstructFieldmapInputSpec(TraitedSpec):
in_coeffs = InputMultiObject(
File(exists=True), mandatory=True, desc="SDCflows-style spline coefficient files"
)
target_ref_file = File(exists=True, mandatory=True, desc="Image to reconstruct the field in alignment with")
fmap_ref_file = File(exists=True, mandatory=True, desc="Reference file aligned with coefficients")
target_ref_file = File(
exists=True, mandatory=True, desc="Image to reconstruct the field in alignment with"
)
fmap_ref_file = File(
exists=True, mandatory=True, desc="Reference file aligned with coefficients"
)
transforms = InputMultiObject(
File(exists=True), mandatory=True, desc="Transform files, from in_file to ref_file (image mode)"
File(exists=True),
mandatory=True,
desc="Transform files, from in_file to ref_file (image mode)",
)
inverse = InputMultiObject(
traits.Bool,
Expand Down