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ENH: Restore resampling to T1w target #3116

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merged 19 commits into from
Oct 26, 2023
Merged

ENH: Restore resampling to T1w target #3116

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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
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RF: Move coordinate copies into threads to delay allocation
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@effigies
effigies committed Oct 23, 2023
commit 333a8fea73bd2a904d2cbe7444efdda84eb9480f
5 changes: 4 additions & 1 deletion fmriprep/interfaces/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -275,6 +275,9 @@ def resample_vol(
coordinates = nb.affines.apply_affine(
hmc_xfm, coordinates.reshape(coords_shape[0], -1).T
).T.reshape(coords_shape)
else:
# Copy coordinates to avoid interfering with other calls
coordinates = coordinates.copy()

vsm = fmap_hz * pe_info[1]
coordinates[pe_info[0], ...] += vsm
Expand Down Expand Up @@ -377,7 +380,7 @@ async def resample_series_async(
partial(
resample_vol,
data=volume,
coordinates=coordinates.copy(),
coordinates=coordinates,
pe_info=pe_info[volid],
hmc_xfm=hmc_xfms[volid] if hmc_xfms else None,
fmap_hz=fmap_hz,
Expand Down