update notebooks

nih-fmrif · Feb 2, 2024 · fd200e7 · fd200e7
1 parent 46415c8
commit fd200e7
Show file tree

Hide file tree

Showing 3 changed files with 222 additions and 28,724 deletions.
diff --git a/notebooks/generate_and_evaluate_targets.ipynb b/notebooks/generate_and_evaluate_targets.ipynb
@@ -25,7 +25,7 @@
     "from nibabel import cifti2 as ci\n",
     "from contarg.normgrid import load_liston_surfs, Surface\n",
     "# from contarg.stimgrid import run_opt_and_save_outputs\n",
-    "from contarg.utils import graph_from_triangles, get_stimroi_path, surf_data_from_cifti, load_timeseries, SurfROI, cross_spearman\n",
+    "from contarg.utils import graph_from_triangles, get_stimroi_path, surf_data_from_cifti, load_timeseries, SurfROI, cross_spearman, replace_cifti_data\n",
     "# from contarg.utils import get_stimroi_path, get_refroi_path, graph_from_triangles, , new_cifti_like, surf_data_from_cifti, cross_spearman, load_timeseries, find_bids_files, add_censor_columns, select_confounds, make_rel_symlink\n",
     "from scipy import stats\n",
     "from scipy.spatial.distance import pdist, cdist\n",
@@ -383,6 +383,35 @@
     "]"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## This is the output you need for targeting"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "stim_stats_rev.sort_values('rep_rva_rank').loc[:, ses_comp_cols].head(10)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "markdown",
+   "source": [
+    "## The rest of this coe is for comparing sessions"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "code",
    "execution_count": 6,

diff --git a/notebooks/prep_normgrid_targeting.ipynb b/notebooks/prep_normgrid_targeting.ipynb
@@ -20,7 +20,8 @@
     "    setup_uncert_sims,\n",
     "    run_clusters,\n",
     "    calc_stimgrid,\n",
-    "    make_uncert_sims\n",
+    "    make_uncert_sims,\n",
+    "    make_uncert_surfaces\n",
     ")"
    ]
   },
@@ -740,20 +741,16 @@
     "                '--njobs',\n",
     "                f'20',\n",
     "                '--thresh-type=mt',\n",
-    "                '--min-thresh=50',\n",
-    "                '--max-thresh=80',\n",
-    "                '--max-mt=80',\n",
+    "                f'--min-thresh={mt_thresh}',\n",
+    "                f'--max-thresh={maxMT}',\n",
+    "                f'--max-mt={maxMT}',\n",
     "            ]\n",
     "            cmds.append(' '.join(cmd))"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": 24,
-   "id": "9179d2aa-aa4a-40cd-9703-1d148e943717",
-   "metadata": {
-    "tags": []
-   },
    "outputs": [
     {
      "data": {
@@ -768,47 +765,14 @@
    ],
    "source": [
     "cmds[0]"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": 29,
-   "id": "4da24ca1-db3f-4da1-bab3-48d128aea1e9",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [],
-   "source": [
-    "!rm -rf /lscratch/$SLURM_JOB_ID/uncertsim-0"
-   ]
-  },
-  {
-   "cell_type": "code",
-   "execution_count": null,
-   "id": "b3a7af00-6223-4f66-b9d9-07beddcdcbc9",
-   "metadata": {
-    "tags": []
-   },
-   "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "[Parallel(n_jobs=20)]: Using backend LokyBackend with 20 concurrent workers.\n"
-     ]
-    }
    ],
-   "source": [
-    "! {cmds[0]}"
-   ]
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "code",
    "execution_count": 28,
-   "id": "7959e330-0f81-4248-a1e0-731837b851ab",
-   "metadata": {
-    "tags": []
-   },
    "outputs": [
     {
      "data": {
@@ -823,7 +787,10 @@
    ],
    "source": [
     "len(cmds)"
-   ]
+   ],
+   "metadata": {
+    "collapsed": false
+   }
   },
   {
    "cell_type": "code",
@@ -909,6 +876,62 @@
     "    print(jobid)"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "source": [
+    " # Create surfaces from uncertainty sims"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "all_settings = []\n",
+    "for subject in subjects:\n",
+    "    sim_dir = Path(anat_dir / f'sub-{subject}/Simulation/simulation-00')\n",
+    "    if not sim_dir.exists():\n",
+    "        sim_dir = Path(anat_dir / f'sub-{subject}/Simulation/simulation-01')\n",
+    "        if not sim_dir.exists():\n",
+    "            print(f\"{sim_dir} not found, skipping\")\n",
+    "    uncert_dir = sim_dir / f'uncert{nsims}'\n",
+    "    settings_path = uncert_dir / 'settings.pkl.gz'\n",
+    "    all_settings.append(settings_path)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "\n",
+    "jobs = []\n",
+    "for (subject, settings_path) in zip(subjects, all_settings):\n",
+    "    src_surf_dir = liston_root / f'sub-{subject}/anat/T1w/fsaverage_LR32k/'\n",
+    "    uncert_dir = settings_path.parent\n",
+    "    jobs.append(delayed(make_uncert_surfaces)(subject, src_surf_dir, uncert_dir, overwrite=True))\n"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "outputs": [],
+   "source": [
+    "Parallel(n_jobs=10, verbose=10)(jobs)"
+   ],
+   "metadata": {
+    "collapsed": false
+   }
+  },
   {
    "cell_type": "markdown",
    "id": "f7a03ef7-64be-4f5d-86f0-bce215da0d7d",