added spm12 standalone installer; and script to extract timings from dicom files

README.rst

@@ -186,3 +186,5 @@ Common problems and fixes
 =========================
 * libXp.so.6 missing (in ubuntu >= 15.10, for example)
 This is a known is http://askubuntu.com/questions/719839/libxp-so-6-missing-15-10. The idea is to install it manually from official sources https://launchpad.net/ubuntu/wily/+package/libxp6
+
+* Beware: the pathname for "scratch" (directory for cache) must not contain any space character! This triggered a nasty bug in nipype....

continuous_integration/install_spm12.sh

@@ -0,0 +1,47 @@
+#! /bin/bash
+set -e
+
+# set -x  # echo on
+
+SPM_ROOT_DIR=~/opt/spm12   #  Installation directory
+
+SPM_SRC=spm12_r6685.zip
+MCRINST=MCRInstaller.bin
+
+mkdir -p $SPM_ROOT_DIR && cd $SPM_ROOT_DIR
+
+if [ ! -d spm12 ]; then
+    if [ ! -f ${SPM_SRC} ]; then 
+	wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/${SPM_SRC}
+    fi
+    unzip -q ${SPM_SRC}
+    chmod 755 spm12/run_spm12.sh
+fi
+
+if [ ! -d mcr ]; then
+    if [ ! -f MCRInstaller.bin ]; then
+	wget http://www.fil.ion.ucl.ac.uk/spm/download/restricted/utopia/MCR/glnxa64/${MCRINST}
+    fi
+    chmod 755 ${MCRINST}
+    ./${MCRINST} -P bean421.installLocation="mcr" -silent
+fi
+
+
+if [ ! -f $SPM_ROOT_DIR/spm12.sh ]; then
+    cat <<EOF > $SPM_ROOT_DIR/spm12.sh
+#!/bin/bash
+SPM12_STANDALONE_HOME=$SPM_ROOT_DIR/spm12
+exec "\${SPM12_STANDALONE_HOME}/run_spm12.sh" "\${SPM12_STANDALONE_HOME}/../mcr/v713" \${1+"\$@"}
+EOF
+
+    chmod 755 $SPM_ROOT_DIR/spm12.sh
+fi
+
+# Create CTF
+$SPM_ROOT_DIR/spm12.sh quit
+cmds="export SPM_DIR=$SPM_ROOT_DIR/spm12/; export SPM_MCR=$SPM_ROOT_DIR/spm12.sh"
+${cmds}
+echo "You may want to add the following commands (the exports) to your ~/.bashrc file once and for all."
+echo
+echo ${cmds}
+

pypreprocess/nipype_preproc_spm_utils.py

@@ -143,20 +143,19 @@ def _do_subject_slice_timing(subject_data, TR, TA=None, spm_dir=None,
 
     # compute nslices
     nslices = load_vols(subject_data.func[0])[0].shape[2]
-    assert 1 <= ref_slice <= nslices, ref_slice
+#    assert 1 <= ref_slice <= nslices, ref_slice
 
-    # compute slice indices / order
-    if not isinstance(slice_order, basestring):
-        slice_order = np.array(slice_order) - 1
-    slice_order = get_slice_indices(nslices, slice_order=slice_order,
-                                    interleaved=interleaved)
+#    # compute slice indices / order
+#    if not isinstance(slice_order, basestring):
+#        slice_order = np.array(slice_order) - 1
+#    slice_order = get_slice_indices(nslices, slice_order=slice_order,
+#                                    inter  leaved=interleaved)
 
     # use pure python (pp) code ?
     if software == "python":
         return _pp_do_subject_slice_timing(subject_data, ref_slice=ref_slice,
                                            slice_order=slice_order,
-                                           caching=caching)
-
+                                           caching=caching)                                 
     # sanitize software choice
     if software != "spm":
         raise NotImplementedError(
@@ -193,8 +192,9 @@ def _do_subject_slice_timing(subject_data, TR, TA=None, spm_dir=None,
     for sess_func in subject_data.func:
         stc_result = stc(in_files=sess_func, time_repetition=TR,
                          time_acquisition=TA, num_slices=nslices,
-                         ref_slice=ref_slice + 1,
-                         slice_order=list(slice_order + 1),  # SPM
+                         ref_slice=ref_slice,
+                         #slice_order=list(slice_order + 1),  # SPM8 ?
+                         slice_order=[int(x) for x in slice_order.split()],  # SPM12
                          ignore_exception=False
                          )
         if stc_result.outputs is None:

scripts/extract_timings.py

@@ -0,0 +1,39 @@
+#! /usr/bin/env python
+# Time-stamp: <2016-05-31 14:58:27 chrplr>
+#
+
+""" Extracts slice timing information from a dicom file.
+To be passed  as argument to slice_order for slice timing correction algorithms """
+
+from __future__ import print_function
+import os
+import glob
+import dicom
+import sys
+
+try:
+    dicom_path = sys.argv[1]
+
+    if os.path.isdir(dicom_path):
+        dicom_ref = sorted(glob.glob(os.path.join(dicom_path, '*.dcm')))[4]
+    else:
+        if (os.path.isfile(dicom_path)):
+            dicom_ref = dicom_path
+
+    TR = dicom.read_file(dicom_ref).RepetitionTime
+    slice_times = dicom.read_file(dicom_ref)[0x19, 0x1029].value
+    nb_slices = len(slice_times)
+
+except:
+    print("Unexpected error: %s" % sys.exc_info()[0])
+    print("\nUsage:\n    %s dicom_path\nWhere dicom_path is a dicom directory" % sys.argv[0])
+    sys.exit(-1)
+
+print("TR = %.3f" % (TR/1000.))
+#print("nb_slices = %d" % nb_slices)
+print("slice_timings = ", end=" ")
+for v in slice_times:
+    print("%.1f" % v, end=" ")
+print("\n", end="")
+print("refslice = %.3f" % (TR/2000.))
+