diff --git a/fmriprep/interfaces/resampling.py b/fmriprep/interfaces/resampling.py
index e6162b0e2..9e40aee62 100644
--- a/fmriprep/interfaces/resampling.py
+++ b/fmriprep/interfaces/resampling.py
@@ -569,7 +569,7 @@ def resample_image(
         hmc = []
 
     # Retrieve the RAS coordinates of the target space
-    coordinates = nt.base.SpatialReference.factory(target).ndcoords.astype('f4').T
+    coordinates = nt.base.SpatialReference.factory(target).ndcoords.astype('f4')
 
     # We will operate in voxel space, so get the source affine
     vox2ras = source.affine
diff --git a/pyproject.toml b/pyproject.toml
index d83f07b0f..a94806386 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -22,15 +22,15 @@ requires-python = ">=3.10"
 dependencies = [
     "acres >= 0.2.0",
     "looseversion >= 1.3",
-    "nibabel >= 4.0.1",
-    "nipype >= 1.8.5",
+    "nibabel >= 5.1.1",
+    "nipype >= 1.9.0",
     "nireports >= 24.1.0",
     "nitime >= 0.9",
-    "nitransforms >= 24.1.1",
+    "nitransforms >= 25.0.1",
     "niworkflows @ git+https://github.com/nipreps/niworkflows.git@master",
-    "numpy >= 1.24",
+    "numpy >= 2.0",
     "packaging >= 24",
-    "pandas >= 1.2",
+    "pandas >= 2.2",
     "psutil >= 5.4",
     "pybids >= 0.16",
     "requests >= 2.27",
@@ -38,7 +38,7 @@ dependencies = [
     "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
     "tedana >= 25.0.0",
     "templateflow >= 24.2.2",
-    "transforms3d >= 0.4",
+    "transforms3d >= 0.4.2",
     "toml >= 0.10",
     "codecarbon >= 2",
     "APScheduler >= 3.10",
diff --git a/requirements.txt b/requirements.txt
index bdf3192a0..db18f7d12 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,5 +1,5 @@
 # This file was autogenerated by uv via the following command:
-#    uv pip compile --extra=container --strip-extras pyproject.toml -c constraints.txt -o requirements.txt -p 3.12
+#    uv pip compile --extra=container --strip-extras pyproject.toml -o requirements.txt -p 3.12 --python-platform linux
 acres==0.3.0
     # via
     #   fmriprep (pyproject.toml)
@@ -68,7 +68,9 @@ contourpy==1.3.2
     #   bokeh
     #   matplotlib
 cryptography==45.0.4
-    # via jwcrypto
+    # via
+    #   jwcrypto
+    #   secretstorage
 cycler==0.12.1
     # via matplotlib
 datalad==1.2.0
@@ -100,6 +102,8 @@ frozendict==2.4.6
     # via pybids
 fsspec==2025.5.1
     # via universal-pathlib
+greenlet==3.2.4
+    # via sqlalchemy
 h11==0.16.0
     # via httpcore
 h5py==3.14.0
@@ -135,6 +139,10 @@ jaraco-context==6.0.1
     #   keyrings-alt
 jaraco-functools==4.1.0
     # via keyring
+jeepney==0.9.0
+    # via
+    #   keyring
+    #   secretstorage
 jinja2==3.1.6
     # via
     #   bokeh
@@ -234,20 +242,18 @@ nipype==1.10.0
     #   smriprep
 nireports==25.2.0
     # via
-    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   sdcflows
+    #   smriprep
 nitime==0.11
     # via fmriprep (pyproject.toml)
-nitransforms==24.1.2
+nitransforms==25.0.1
     # via
-    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   niworkflows
     #   sdcflows
 niworkflows==1.13.4
     # via
-    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   sdcflows
     #   smriprep
@@ -441,14 +447,14 @@ scipy==1.15.2
     #   sdcflows
     #   tedana
 sdcflows==2.13.2
-    # via
-    #   -c constraints.txt
-    #   fmriprep (pyproject.toml)
+    # via fmriprep (pyproject.toml)
 seaborn==0.13.2
     # via
     #   nireports
     #   niworkflows
     #   tedana
+secretstorage==3.3.3
+    # via keyring
 sentry-sdk==2.28.0
     # via fmriprep (pyproject.toml)
 shellingham==1.5.4
@@ -474,9 +480,8 @@ svgutils==0.3.4
     # via niworkflows
 tedana==25.0.1
     # via fmriprep (pyproject.toml)
-templateflow==24.2.2
+templateflow==25.0.3
     # via
-    #   -c constraints.txt
     #   fmriprep (pyproject.toml)
     #   nireports
     #   niworkflows