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update jupyter notebook
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‎notebooks/saving_stim_files.ipynb‎

Lines changed: 242 additions & 2 deletions
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@@ -9,10 +9,250 @@
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"execution_count": 8,
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"metadata": {},
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"outputs": [],
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"source": []
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"source": [
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"% add the relevant functions from the source and library folder\n",
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"addpath(genpath(fullfile(pwd, '..', 'src')))\n",
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"addpath(genpath(fullfile(pwd, '..', 'lib')))"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Set Up"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 9,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\r\n",
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"\r\n",
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"___________________________________________________\r\n",
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"___________________________________________________\r\n",
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" \r\n",
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" ___ ___ ___ ___ ___ ___ ___ \r\n",
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" / __| _ \\ _ \\ | _ )_ _| \\/ __|\r\n",
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" | (__| _/ _/ | _ \\| || |) \\__ \\\r\n",
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" \\___|_| |_| |___/___|___/|___/\r\n",
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" \r\n",
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"Thank you for using the CPP BIDS - version v2.0.0. \r\n",
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"\r\n",
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"Current list of contributors includes:\r\n",
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" Remi Gau\r\n",
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" Marco Barilari\r\n",
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" Ceren Battal\r\n",
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" Tomas Lenc\r\n",
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"\b\r\n",
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"\r\n",
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"Please cite using the following DOI: \r\n",
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" https://doi.org/10.5281/zenodo.4007674\r\n",
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"\r\n",
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"For bug report, suggestions or contributions see: \r\n",
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" https://github.com/cpp-lln-lab/CPP_BIDS\r\n",
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"\r\n",
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"___________________________________________________\r\n",
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"___________________________________________________\r\n",
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"\r\n",
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"\r\n",
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"\r\n",
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"Data will be saved in this directory:\r\n",
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"\t/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func\r\n",
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"\r\n",
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"Data will be saved in this file:\r\n",
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"\tsub-001_ses-001_task-testTask_run-001_events_date-202012250913.tsv\r\n"
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]
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}
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],
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"source": [
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"cfg.dir.output = fullfile(pwd, 'output');\n",
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"\n",
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"cfg.verbose = 2;\n",
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"\n",
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"cfg.subject.subjectNb = 1;\n",
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"cfg.subject.runNb = 1;\n",
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"\n",
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"cfg.task.name = 'test task';\n",
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"\n",
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"cfg.testingDevice = 'mri';\n",
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"\n",
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"cfg = createFilename(cfg);"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Define the columns of the stim.tsv"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 10,
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"metadata": {},
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"outputs": [],
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"source": [
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"logFile.extraColumns = {'Speed', 'LHL24', 'is_Fixation'};\n",
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"\n",
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"logFile = saveEventsFile('init_stim', cfg, logFile);\n",
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"\n",
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"logFile.extraColumns.Speed.length = 1;\n",
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"logFile.extraColumns.LHL24.length = 3;\n",
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"logFile.extraColumns.is_Fixation.length = 1;"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 11,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" extraColumns =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" Speed =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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" LHL24 =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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" is_Fixation =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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"\n",
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" onset = 55\n",
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" trial_type = motion_up\n",
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" duration = 66\n",
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" isStim = 1\n",
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" filename = sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
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" fileID = 3\n",
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" Speed = 2\n",
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" LHL24 =\n",
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"\n",
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" 1 2 3\n",
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"\n",
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" is_Fixation = 1\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" extraColumns =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" Speed =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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" LHL24 =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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" is_Fixation =\n",
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"\n",
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" scalar structure containing the fields:\n",
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"\n",
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" bids: 1x1 scalar struct\n",
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" length: 1x1 scalar\n",
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"\n",
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"\n",
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" onset = 55\n",
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" trial_type = motion_up\n",
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" duration = 66\n",
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" isStim = 1\n",
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" filename = sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
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" fileID = 3\n",
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" Speed = 2\n",
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" LHL24 =\n",
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"\n",
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" 1 2 3\n",
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"\n",
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" is_Fixation = 1\n",
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"2.000000\t1.000000\t2.000000\t3.000000\ttrue\t\n",
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"\n",
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"Data were saved in this file:\n",
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"\n",
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"/home/remi/github/CPP_BIDS/notebooks/output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_stim_date-202012250913.tsv\n",
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"\n"
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]
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}
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],
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"source": [
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"% create the events file and header\n",
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"logFile = saveEventsFile('open', cfg, logFile);\n",
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"\n",
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"% ROW 1\n",
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"logFile(1, 1).onset = 55;\n",
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"logFile(end, 1).trial_type = 'motion_up';\n",
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"logFile(end, 1).duration = 66;\n",
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"logFile(end, 1).Speed = 2;\n",
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"logFile(end, 1).LHL24 = 1:3;\n",
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"logFile(end, 1).is_Fixation = true;\n",
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"\n",
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"logFile = saveEventsFile('save', cfg, logFile);\n",
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"\n",
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"% close the file\n",
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"saveEventsFile('close', cfg, logFile);"
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]
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},
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{
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"cell_type": "markdown",
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"metadata": {},
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"source": [
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"## Inspect the content of the stim.tsv file\n",
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" \n",
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"The `onset`, `duration` and `trial_type` are ignored because they were note spcified in the `extraColumns` field.\n"
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]
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},
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{
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"cell_type": "code",
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"execution_count": 13,
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"metadata": {},
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"outputs": [
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{
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"name": "stdout",
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"output_type": "stream",
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"text": [
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"2.000000\t1.000000\t2.000000\t3.000000\ttrue\t\r\n",
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"\n"
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]
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}
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],
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"source": [
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"!cat output/source/sub-001/ses-001/func/sub-001_ses-001_task-testTask_run-001_stim_date-*.tsv "
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]
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}
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],
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"metadata": {

‎requirements.txt‎

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@@ -2,4 +2,6 @@ Sphinx
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sphinxcontrib-matlabdomain
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sphinxcontrib-napoleon
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sphinx_rtd_theme
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miss_hit==0.9.15
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miss_hit==0.9.15
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notebook
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octave_kernel

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