{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Compare Hippocampal Subfield Volumes Computed By ASHS & Freesurfer\n", "\n", "NOTE: Dummy data with pseudo volumes" ] }, { "cell_type": "code", "execution_count": 1, "metadata": {}, "outputs": [], "source": [ "SUBJECTS_DIR = '../tests/subjects'\n", "SUBJECT = 'bert'" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Read Volume Files" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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subjectsource_typesource_basename
0bertASHSbert_left_corr_nogray_volumes.txt
1bertASHSbert_left_corr_usegray_volumes.txt
2bertASHSbert_left_heur_volumes.txt
3bertASHSbert_right_corr_nogray_volumes.txt
4bertFreesurferlh.hippoSfVolumes-T1-T2.v10.txt
5bertFreesurferlh.hippoSfVolumes-T1.v10.txt
\n", "
" ], "text/plain": [ " subject source_type source_basename\n", "0 bert ASHS bert_left_corr_nogray_volumes.txt\n", "1 bert ASHS bert_left_corr_usegray_volumes.txt\n", "2 bert ASHS bert_left_heur_volumes.txt\n", "3 bert ASHS bert_right_corr_nogray_volumes.txt\n", "4 bert Freesurfer lh.hippoSfVolumes-T1-T2.v10.txt\n", "5 bert Freesurfer lh.hippoSfVolumes-T1.v10.txt" ] }, "execution_count": 2, "metadata": {}, "output_type": "execute_result" } ], "source": [ "import os, pandas\n", "from freesurfer_volume_reader import SubfieldVolumeFile, ashs, freesurfer\n", "\n", "def read_volume_file(volume_file: SubfieldVolumeFile) -> pandas.DataFrame:\n", " volume_frame = volume_file.read_volumes_dataframe()\n", " volume_frame['source_basename'] = os.path.basename(volume_file.absolute_path)\n", " return volume_frame\n", "\n", "def find_read_volume_files(source_type: str, volume_type) -> pandas.DataFrame:\n", " volume_files = filter(lambda f: f.subject == SUBJECT, volume_type.find(SUBJECTS_DIR))\n", " frame = pandas.concat(map(read_volume_file, volume_files))\n", " frame['source_type'] = source_type\n", " return frame\n", "\n", "volume_frame = pandas.concat([find_read_volume_files('ASHS', ashs.HippocampalSubfieldsVolumeFile),\n", " find_read_volume_files('Freesurfer', freesurfer.HippocampalSubfieldsVolumeFile)],\n", " sort=False)\n", "volume_frame[['subject', 'source_type', 'source_basename']].drop_duplicates() \\\n", " .sort_values(by='source_basename').reset_index(drop=True)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Select Subfields Provided by Both ASHS & Freesurfer" ] }, { "cell_type": "code", "execution_count": 3, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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source_typesubfield
0ASHSCA1
1ASHSCA2+3
2ASHSDG
3ASHSERC
4ASHSPHC
5ASHSPRC
6ASHSSUB
7FreesurferCA1
8FreesurferCA3
9FreesurferCA4
10FreesurferGC-ML-DG
11FreesurferHATA
12FreesurferHippocampal_tail
13FreesurferWhole_hippocampus
14Freesurferfimbria
15Freesurferhippocampal-fissure
16Freesurfermolecular_layer_HP
17Freesurferparasubiculum
18Freesurferpresubiculum
19Freesurfersubiculum
\n", "
" ], "text/plain": [ " source_type subfield\n", "0 ASHS CA1\n", "1 ASHS CA2+3\n", "2 ASHS DG\n", "3 ASHS ERC\n", "4 ASHS PHC\n", "5 ASHS PRC\n", "6 ASHS SUB\n", "7 Freesurfer CA1\n", "8 Freesurfer CA3\n", "9 Freesurfer CA4\n", "10 Freesurfer GC-ML-DG\n", "11 Freesurfer HATA\n", "12 Freesurfer Hippocampal_tail\n", "13 Freesurfer Whole_hippocampus\n", "14 Freesurfer fimbria\n", "15 Freesurfer hippocampal-fissure\n", "16 Freesurfer molecular_layer_HP\n", "17 Freesurfer parasubiculum\n", "18 Freesurfer presubiculum\n", "19 Freesurfer subiculum" ] }, "execution_count": 3, "metadata": {}, "output_type": "execute_result" } ], "source": [ "volume_frame[['source_type', 'subfield']].drop_duplicates() \\\n", " .sort_values(by=['source_type', 'subfield']).reset_index(drop=True)" ] }, { "cell_type": "code", "execution_count": 4, "metadata": {}, "outputs": [ { "data": { "text/plain": [ "{'CA1', 'subiculum'}" ] }, "execution_count": 4, "metadata": {}, "output_type": "execute_result" } ], "source": [ "volume_frame['subfield'].replace('SUB', 'subiculum', inplace=True)\n", "\n", "common_subfields = set.intersection(*(set(volume_frame[volume_frame['source_type'] == src]['subfield'].unique())\n", " for src in volume_frame['source_type'].unique()))\n", "common_subfields" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "## Compare Volumes" ] }, { "cell_type": "code", "execution_count": 5, "metadata": {}, "outputs": [ { "data": { "text/html": [ "
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segmentation_modeASHS T1 & T2 heurASHS T1 & T2 nograyASHS T1 & T2 usegrayFreesurfer T1Freesurfer T1 & T2
subfieldhemisphere
CA1left678.903678.901678.90234.56789144.567891
rightNaN678.903NaNNaNNaN
subiculumleft457.781457.789457.780234.567891244.567891
rightNaN457.781NaNNaNNaN
\n", "
" ], "text/plain": [ "segmentation_mode ASHS T1 & T2 heur ASHS T1 & T2 nogray \\\n", "subfield hemisphere \n", "CA1 left 678.903 678.901 \n", " right NaN 678.903 \n", "subiculum left 457.781 457.789 \n", " right NaN 457.781 \n", "\n", "segmentation_mode ASHS T1 & T2 usegray Freesurfer T1 Freesurfer T1 & T2 \n", "subfield hemisphere \n", "CA1 left 678.902 34.567891 44.567891 \n", " right NaN NaN NaN \n", "subiculum left 457.780 234.567891 244.567891 \n", " right NaN NaN NaN " ] }, "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ "common_subfields_frame = volume_frame[volume_frame['subfield'].isin(common_subfields)].copy()\n", "\n", "def generate_segmentation_mode(row) -> str:\n", " if row['source_type'] == 'ASHS':\n", " return 'ASHS T1 & T2 {}'.format(row['correction'] or 'heur')\n", " if row['source_type'] == 'Freesurfer':\n", " abrev_analysis_id = row['analysis_id'].split('_')[0][:7] if row['analysis_id'] else None\n", " return 'Freesurfer ' + ' & '.join(filter(None, ['T1' if row['T1_input'] else None, abrev_analysis_id]))\n", " raise TypeError(row['source_type'])\n", "\n", "\n", "common_subfields_frame['segmentation_mode'] = common_subfields_frame.apply(generate_segmentation_mode, axis=1)\n", "\n", "common_subfields_frame.pivot_table(values='volume_mm^3',\n", " index=['subfield', 'hemisphere'],\n", " columns='segmentation_mode')" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ "NOTE: Dummy data with pseudo volumes" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, "outputs": [ { "data": { "application/javascript": [ "/* Put everything inside the global mpl namespace */\n", "window.mpl = {};\n", "\n", "\n", "mpl.get_websocket_type = function() {\n", " if (typeof(WebSocket) !== 'undefined') {\n", " return WebSocket;\n", " } else if (typeof(MozWebSocket) !== 'undefined') {\n", " return MozWebSocket;\n", " } else {\n", " alert('Your browser does not have WebSocket support.' +\n", " 'Please try Chrome, Safari or Firefox ≥ 6. ' +\n", " 'Firefox 4 and 5 are also supported but you ' +\n", " 'have to enable WebSockets in about:config.');\n", " };\n", "}\n", "\n", "mpl.figure = function(figure_id, websocket, ondownload, parent_element) {\n", " this.id = figure_id;\n", "\n", " this.ws = websocket;\n", "\n", " this.supports_binary = (this.ws.binaryType != undefined);\n", "\n", " if (!this.supports_binary) {\n", " var warnings = document.getElementById(\"mpl-warnings\");\n", " if (warnings) {\n", " warnings.style.display = 'block';\n", " warnings.textContent = (\n", " \"This browser does not support binary websocket messages. \" +\n", " \"Performance may be slow.\");\n", " }\n", " }\n", "\n", " this.imageObj = new Image();\n", "\n", " this.context = undefined;\n", " this.message = undefined;\n", " this.canvas = undefined;\n", " this.rubberband_canvas = undefined;\n", " this.rubberband_context = undefined;\n", " this.format_dropdown = undefined;\n", "\n", " this.image_mode = 'full';\n", "\n", " this.root = $('
');\n", " this._root_extra_style(this.root)\n", " this.root.attr('style', 'display: inline-block');\n", "\n", " $(parent_element).append(this.root);\n", "\n", " this._init_header(this);\n", " this._init_canvas(this);\n", " this._init_toolbar(this);\n", "\n", " var fig = this;\n", "\n", " this.waiting = false;\n", "\n", " this.ws.onopen = function () {\n", " fig.send_message(\"supports_binary\", {value: fig.supports_binary});\n", " fig.send_message(\"send_image_mode\", {});\n", " if (mpl.ratio != 1) {\n", " fig.send_message(\"set_dpi_ratio\", {'dpi_ratio': mpl.ratio});\n", " }\n", " fig.send_message(\"refresh\", {});\n", " }\n", "\n", " this.imageObj.onload = function() {\n", " if (fig.image_mode == 'full') {\n", " // Full images could contain transparency (where diff images\n", " // almost always do), so we need to clear the canvas so that\n", " // there is no ghosting.\n", " fig.context.clearRect(0, 0, fig.canvas.width, fig.canvas.height);\n", " }\n", " fig.context.drawImage(fig.imageObj, 0, 0);\n", " };\n", "\n", " this.imageObj.onunload = function() {\n", " fig.ws.close();\n", " }\n", "\n", " this.ws.onmessage = this._make_on_message_function(this);\n", "\n", " this.ondownload = ondownload;\n", "}\n", "\n", "mpl.figure.prototype._init_header = function() {\n", " var titlebar = $(\n", " '
');\n", " var titletext = $(\n", " '
');\n", " titlebar.append(titletext)\n", " this.root.append(titlebar);\n", " this.header = titletext[0];\n", "}\n", "\n", "\n", "\n", "mpl.figure.prototype._canvas_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "\n", "mpl.figure.prototype._root_extra_style = function(canvas_div) {\n", "\n", "}\n", "\n", "mpl.figure.prototype._init_canvas = function() {\n", " var fig = this;\n", "\n", " var canvas_div = $('
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