FIX: update spm12 folder structure

Author: miykael

notebooks/advanced_spmmcr.ipynb

@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "from nipype.interfaces import spm\n",
-    "matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2018b/v95/ script'\n",
+    "matlab_cmd = '/opt/spm12-r7219/run_spm12.sh /opt/matlabmcr-2010a/v713/ script'\n",
     "spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)"
    ]
   },

notebooks/basic_error_and_crashes.ipynb

@@ -451,7 +451,7 @@
     "\n",
     "```python\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')\n",
+    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')\n",
     "```"
    ]
   },

notebooks/example_normalize.ipynb

@@ -351,7 +351,7 @@
     "# Smoothing withds used during preprocessing\n",
     "fwhm = [4, 8]\n",
     "\n",
-    "template = '/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'"
+    "template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
    ]
   },
   {

notebooks/handson_analysis.ipynb

@@ -50,7 +50,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
    ]
   },
   {
@@ -523,7 +523,7 @@
     "from nipype.interfaces.spm import Normalize12\n",
     "\n",
     "# Location of the template\n",
-    "template = '/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'"
+    "template = '/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'"
    ]
   },
   {
@@ -973,7 +973,7 @@
    "outputs": [],
    "source": [
     "# Load GM probability map of TPM.nii\n",
-    "img = nb.load('/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii')\n",
+    "img = nb.load('/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii')\n",
     "GM_template = nb.Nifti1Image(img.get_data()[..., 0], img.affine, img.header)\n",
     "\n",
     "# Plot normalized subject anatomy\n",
@@ -1042,7 +1042,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
    ]
   },
   {
@@ -1303,7 +1303,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "TEMPLATE='/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
+    "TEMPLATE='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'\n",
     "\n",
     "# Extract the first volume with `fslroi`\n",
     "fslroi $TEMPLATE GM_PM.nii.gz 0 1\n",

notebooks/handson_preprocessing.ipynb

@@ -78,7 +78,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-r7219/spm12_mcr/spm12')"
    ]
   },
   {
@@ -474,7 +474,7 @@
    "outputs": [],
    "source": [
     "# Use the following tissue specification to get a GM and WM probability map\n",
-    "tpm_img ='/opt/spm12-r7219/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
+    "tpm_img ='/opt/spm12-r7219/spm12_mcr/spm12/tpm/TPM.nii'\n",
     "tissue1 = ((tpm_img, 1), 1, (True,False), (False, False))\n",
     "tissue2 = ((tpm_img, 2), 1, (True,False), (False, False))\n",
     "tissue3 = ((tpm_img, 3), 2, (True,False), (False, False))\n",