finalized MACM workflow

NBCLab · Jun 23, 2020 · 4a57e68 · 4a57e68
1 parent 64fcb02
commit 4a57e68
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Showing 5 changed files with 92 additions and 8 deletions.
diff --git a/connectivity/macm.py b/connectivity/macm.py
@@ -3,8 +3,9 @@
 from nimare.meta.cbma import ALE
 from nimare.dataset import Dataset
 from nimare.correct import FWECorrector
-from nimare.io import convert_neurosynth_to_dataset
 
+import sys
+sys.path.append('/Users/miriedel/Desktop/GitHub/niconn/')
 
 def macm_workflow(prefix=None, mask=None, output_dir=None, ns_data_dir=None):
 
@@ -15,7 +16,7 @@ def macm_workflow(prefix=None, mask=None, output_dir=None, ns_data_dir=None):
         raise Exception('A valid directory is required for downloading Neurosynth data!')
 
     if prefix is None:
-        prefix = op.basename(mask_fn).split('.')[0]
+        prefix = op.basename(mask).split('.')[0]
 
     if output_dir is None:
         output_dir = op.dirname(op.abspath(mask))
@@ -24,18 +25,18 @@ def macm_workflow(prefix=None, mask=None, output_dir=None, ns_data_dir=None):
 
     # download neurosynth dataset if necessary
     if not op.isfile(dataset_file):
-        from .datasets import neurosyth.neurosynth_download
+        from datasets.neurosynth import neurosynth_download
         neurosynth_download(ns_data_dir)
 
     dset = Dataset.load(dataset_file)
-    mask_ids = dset.get_studies_by_mask(mask_fn)
+    mask_ids = dset.get_studies_by_mask(mask)
     maskdset = dset.slice(mask_ids)
     nonmask_ids = sorted(list(set(dset.ids) - set(mask_ids)))
     nonmaskdset = dset.slice(nonmask_ids)
 
     ale = ALE(kernel__fwhm=15)
     ale.fit(maskdset)
 
-    corr = FWECorrector(method='permutation', n_iters=10, n_cores=-1, voxel_thresh=0.001)
+    corr = FWECorrector(method='permutation', n_iters=10000, n_cores=-1, voxel_thresh=0.001)
     cres = corr.transform(ale.results)
     cres.save_maps(output_dir=output_dir, prefix=prefix)
diff --git a/datasets/__pycache__/neurosynth.cpython-37.pyc b/datasets/__pycache__/neurosynth.cpython-37.pyc
diff --git a/neurosynth.py → datasets/neurosynth.py b/neurosynth.py → datasets/neurosynth.py
@@ -1,6 +1,8 @@
 import os
 import os.path as op
 from neurosynth.base.dataset import download
+from nimare.io import convert_neurosynth_to_dataset
+
 
 def neurosynth_download(ns_data_dir=None):
 
@@ -11,7 +13,7 @@ def neurosynth_download(ns_data_dir=None):
 
     if not op.isdir(ns_data_dir):
         os.mkdir(ns_data_dir)
-        
+
     download(ns_data_dir, unpack=True)
     ###############################################################################
     # Convert Neurosynth database to NiMARE dataset file

diff --git a/tests/test_macm/ns_hand_roi.nii.gz b/tests/test_macm/ns_hand_roi.nii.gz
diff --git a/tests/test_macm/test_macm_workflow.ipynb b/tests/test_macm/test_macm_workflow.ipynb
@@ -2,13 +2,94 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": null,
+   "execution_count": 1,
    "metadata": {},
-   "outputs": [],
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "ERROR:duecredit:Failed to import duecredit due to No module named 'duecredit'\n"
+     ]
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "200623-06:45:09,54 nipype.utils INFO:\n",
+      "\t Running nipype version 1.4.2 (latest: 1.5.0)\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:nipype.utils:Running nipype version 1.4.2 (latest: 1.5.0)\n"
+     ]
+    }
+   ],
    "source": [
+    "import sys\n",
+    "sys.path.append('/Users/miriedel/Desktop/GitHub/niconn/')\n",
     "from connectivity.macm import macm_workflow"
    ]
   },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "roi = '/Users/miriedel/Desktop/GitHub/niconn/tests/test_macm/ns_hand_roi.nii.gz'\n",
+    "ns_data_dir = '/Users/miriedel/Desktop/GitHub/niconn/tests/test_macm/ns_data_dir'"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "INFO:nimare.correct.base:Using correction method implemented in Estimator: <class 'nimare.meta.cbma.ale.ALE'>.correct_fwe_permutation.\n"
+     ]
+    },
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "3ab771ceaa714913b2bfdee49eb25d4a",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "HBox(children=(FloatProgress(value=0.0, max=10.0), HTML(value='')))"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    },
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "\n"
+     ]
+    },
+    {
+     "name": "stderr",
+     "output_type": "stream",
+     "text": [
+      "/Users/miriedel/Desktop/GitHub/NiMARE/nimare/meta/cbma/ale.py:348: RuntimeWarning: divide by zero encountered in log\n",
+      "  logp_vfwe_values = -np.log(p_fwe_values)\n"
+     ]
+    }
+   ],
+   "source": [
+    "macm_workflow(mask=roi, ns_data_dir=ns_data_dir)"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": null,