ENH: change spm12 path to new location

miykael · miykael · commit aa30290aed96 · 2018-05-18T17:02:58.000+02:00
diff --git a/notebooks/advanced_spmmcr.ipynb b/notebooks/advanced_spmmcr.ipynb
@@ -16,7 +16,7 @@
    "outputs": [],
    "source": [
     "from nipype.interfaces import spm\n",
-    "matlab_cmd = '/opt/spm12/run_spm12.sh /opt/mcr/v92/ script'\n",
+    "matlab_cmd = '/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94/ script'\n",
     "spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)"
    ]
   },
diff --git a/notebooks/basic_error_and_crashes.ipynb b/notebooks/basic_error_and_crashes.ipynb
@@ -451,7 +451,7 @@
     "\n",
     "```python\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/usr/local/MATLAB/R2017a/toolbox/spm12')\n",
+    "MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')\n",
     "```"
    ]
   },
diff --git a/notebooks/example_normalize.ipynb b/notebooks/example_normalize.ipynb
@@ -351,7 +351,7 @@
     "# Smoothing withds used during preprocessing\n",
     "fwhm = [4, 8]\n",
     "\n",
-    "template = '/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii'"
+    "template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
    ]
   },
   {
diff --git a/notebooks/handson_analysis.ipynb b/notebooks/handson_analysis.ipynb
@@ -47,7 +47,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
    ]
   },
   {
@@ -520,7 +520,7 @@
     "from nipype.interfaces.spm import Normalize12\n",
     "\n",
     "# Location of the template\n",
-    "template = '/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii'"
+    "template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"
    ]
   },
   {
@@ -970,7 +970,7 @@
    "outputs": [],
    "source": [
     "# Load GM probability map of TPM.nii\n",
-    "img = nb.load('/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii')\n",
+    "img = nb.load('/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii')\n",
     "GM_template = nb.Nifti1Image(img.get_data()[..., 0], img.affine, img.header)\n",
     "\n",
     "# Plot normalized subject anatomy\n",
@@ -1039,7 +1039,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
    ]
   },
   {
@@ -1300,7 +1300,7 @@
    "outputs": [],
    "source": [
     "%%bash\n",
-    "TEMPLATE='/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
+    "TEMPLATE='/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
     "\n",
     "# Extract the first volume with `fslroi`\n",
     "fslroi $TEMPLATE GM_PM.nii.gz 0 1\n",
diff --git a/notebooks/handson_preprocessing.ipynb b/notebooks/handson_preprocessing.ipynb
@@ -75,7 +75,7 @@
     "\n",
     "# Specify which SPM to use\n",
     "from nipype.interfaces.matlab import MatlabCommand\n",
-    "MatlabCommand.set_default_paths('/opt/spm12/spm12_mcr/spm/spm12')"
+    "MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')"
    ]
   },
   {
@@ -471,7 +471,7 @@
    "outputs": [],
    "source": [
     "# Use the following tissue specification to get a GM and WM probability map\n",
-    "tpm_img ='/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii'\n",
+    "tpm_img ='/opt/spm12-dev/spm12_mcr/spm/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",

Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,7 @@`
`16`	`16`	`"outputs": [],`
`17`	`17`	`"source": [`
`18`	`18`	`"from nipype.interfaces import spm\n",`
`19`		`- "matlab_cmd = '/opt/spm12/run_spm12.sh /opt/mcr/v92/ script'\n",`
	`19`	`+ "matlab_cmd = '/opt/spm12-dev/run_spm12.sh /opt/matlabmcr-2018a/v94/ script'\n",`
`20`	`20`	`"spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True)"`
`21`	`21`	`]`
`22`	`22`	`},`
Original file line number	Diff line number	Diff line change
`@@ -451,7 +451,7 @@`
`451`	`451`	`"\n",`
`452`	`452`	"```python\n",
`453`	`453`	`"from nipype.interfaces.matlab import MatlabCommand\n",`
`454`		`- "MatlabCommand.set_default_paths('/usr/local/MATLAB/R2017a/toolbox/spm12')\n",`
	`454`	`+ "MatlabCommand.set_default_paths('/opt/spm12-dev/spm12_mcr/spm/spm12')\n",`
`455`	`455`	"```"
`456`	`456`	`]`
`457`	`457`	`},`
Original file line number	Diff line number	Diff line change
`@@ -351,7 +351,7 @@`
`351`	`351`	`"# Smoothing withds used during preprocessing\n",`
`352`	`352`	`"fwhm = [4, 8]\n",`
`353`	`353`	`"\n",`
`354`		`- "template = '/opt/spm12/spm12_mcr/spm/spm12/tpm/TPM.nii'"`
	`354`	`+ "template = '/opt/spm12-dev/spm12_mcr/spm/spm12/tpm/TPM.nii'"`
`355`	`355`	`]`
`356`	`356`	`},`
`357`	`357`	`{`