diff --git a/pkgs/development/python-modules/nibabel/default.nix b/pkgs/development/python-modules/nibabel/default.nix
index 979f12c8d9857d..3a907bc8ca027d 100644
--- a/pkgs/development/python-modules/nibabel/default.nix
+++ b/pkgs/development/python-modules/nibabel/default.nix
@@ -1,31 +1,28 @@
 { lib
 , buildPythonPackage
 , fetchPypi
-, isPy3k
 , isPy27
-, bz2file
-, mock
 , nose
+, pytest
 , numpy
-, six
+, h5py
+, pydicom
+, scipy
 }:
 
 buildPythonPackage rec {
   pname = "nibabel";
-  version = "3.0.0";
+  version = "3.0.1";
   disabled = isPy27;
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "0f5bc325c9cb203c6f0ab876ba1a5ada811284bb3a4c5d063eeaafaefbad873d";
+    sha256 = "08nlny8vzkpjpyb0q943cq57m2s4wndm86chvd3d5qvar9z6b36k";
   };
 
-  propagatedBuildInputs = [
-    numpy
-    six
-  ] ++ lib.optional (!isPy3k) bz2file;
+  propagatedBuildInputs = [ numpy scipy h5py pydicom ];
 
-  checkInputs = [ nose mock ];
+  checkInputs = [ nose pytest ];
 
   checkPhase = ''
     nosetests
@@ -36,5 +33,6 @@ buildPythonPackage rec {
     description = "Access a multitude of neuroimaging data formats";
     license = licenses.mit;
     maintainers = with maintainers; [ ashgillman ];
+    platforms = platforms.x86_64;  # https://github.com/nipy/nibabel/issues/861
   };
 }
diff --git a/pkgs/development/python-modules/nilearn/default.nix b/pkgs/development/python-modules/nilearn/default.nix
index 9158ee77e508d4..a379f236f3f0b2 100644
--- a/pkgs/development/python-modules/nilearn/default.nix
+++ b/pkgs/development/python-modules/nilearn/default.nix
@@ -1,5 +1,5 @@
-{ stdenv, buildPythonPackage, fetchPypi, nose, nibabel, numpy, scikitlearn
-, scipy, matplotlib }:
+{ stdenv, buildPythonPackage, fetchPypi, pytest
+, nibabel, numpy, pandas, scikitlearn, scipy, matplotlib, joblib }:
 
 buildPythonPackage rec {
   pname = "nilearn";
@@ -10,19 +10,24 @@ buildPythonPackage rec {
     sha256 = "07eb764f2b7b39b487f806a067e394d8ebffff21f57cd1ecdb5c4030b7210210";
   };
 
+  postPatch = ''
+    substituteInPlace setup.py --replace "required_packages.append('sklearn')" ""
+  '';
+  # https://github.com/nilearn/nilearn/issues/2288
+
   # disable some failing tests
   checkPhase = ''
-    nosetests nilearn/tests \
-    -e test_cache_mixin_with_expand_user -e test_clean_confounds -e test_detrend \
-    -e test_clean_detrending -e test_high_variance_confounds
+    pytest nilearn/tests -k 'not test_cache_mixin_with_expand_user'  # accesses ~/
   '';
 
-  checkInputs = [ nose ];
+  checkInputs = [ pytest ];
 
   propagatedBuildInputs = [
+    joblib
     matplotlib
     nibabel
     numpy
+    pandas
     scikitlearn
     scipy
   ];
diff --git a/pkgs/development/python-modules/pydicom/default.nix b/pkgs/development/python-modules/pydicom/default.nix
index d281193be2319a..639bd99da33b5f 100644
--- a/pkgs/development/python-modules/pydicom/default.nix
+++ b/pkgs/development/python-modules/pydicom/default.nix
@@ -8,12 +8,12 @@
 }:
 
 buildPythonPackage rec {
-  version = "1.3.0";
+  version = "1.4.1";
   pname = "pydicom";
 
   src = fetchPypi {
     inherit pname version;
-    sha256 = "1j11lsykqbnw9d6gzgj6kfn6lawvm5d9azd9palj3l1xhj0hlnsq";
+    sha256 = "0ki4736h6mp77733rsrwicl8pyig39idywzcmwvw3nzi2r1yc7w8";
   };
 
   propagatedBuildInputs = [ numpy pillow ];