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2 changes: 1 addition & 1 deletion docs/html/.buildinfo
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# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
config: 465c02c6e0a9948a0a55a33d44030df7
config: d36473da3884bbc8cf47252bf979551f
tags: 645f666f9bcd5a90fca523b33c5a78b7
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16 changes: 8 additions & 8 deletions docs/html/_modules/index.html
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<!DOCTYPE html>

<html lang="en" data-content_root="../">
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Overview: module code &#8212; mia_processes 2.6.1-dev+d3e43d68 documentation</title>
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=f63d8bfa" />
<link rel="stylesheet" type="text/css" href="../_static/haiku.css?v=e491ac2d" />
<script src="../_static/documentation_options.js?v=717c3d5b"></script>
<title>Overview: module code &#8212; mia_processes 2.6.1-dev+aa446e49 documentation</title>
<link rel="stylesheet" type="text/css" href="../_static/pygments.css?v=659b1fac" />
<link rel="stylesheet" type="text/css" href="../_static/haiku.css?v=d31ea6cb" />
<script data-url_root="../" id="documentation_options" src="../_static/documentation_options.js?v=593635bf"></script>
<script src="../_static/doctools.js?v=888ff710"></script>
<script src="../_static/sphinx_highlight.js?v=dc90522c"></script>
<script src="../_static/sphinx_highlight.js?v=4825356b"></script>
<link rel="index" title="Index" href="../genindex.html" />
<link rel="search" title="Search" href="../search.html" />
</head><body>
<div class="header" role="banner"><h1 class="heading"><a href="../index.html">
<span>mia_processes 2.6.1-dev+d3e43d68 documentation</span></a></h1>
<span>mia_processes 2.6.1-dev+aa446e49 documentation</span></a></h1>
<h2 class="heading"><span>Overview: module code</span></h2>
</div>
<div class="topnav" role="navigation" aria-label="top navigation">
Expand Down Expand Up @@ -77,7 +77,7 @@ <h1>All modules for which code is available</h1>

<div class="footer" role="contentinfo">
&#169; Copyright 2019, populse.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.2.6.
Created using <a href="https://www.sphinx-doc.org/">Sphinx</a> 7.1.2.
</div>
</body>
</html>
420 changes: 99 additions & 321 deletions docs/html/_modules/mia_processes/bricks/tools/tools.html

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Expand Up @@ -24,7 +24,7 @@ For bloc design, the csv file should contains two columns by conditions: one wit
The first row of the column with the onset should contains the name of the condition
and the first row of the column with the duration should contain the name of the condition + " duration":

.. image:: ../../images/getConditionsFromCSV_bloc_example.png
.. image:: ../../images/getRegressorsFromCSV_example.png
:width: 300
:alt: csv example bloc design

Expand All @@ -40,7 +40,7 @@ and the first row of the column with the duration should contain the name of the
::

ex. ['/home/username/MIA_projects/data/downloaded_data/sess01_bloc_onset.csv',
'/home/username/MIA_projects//data/downloaded_data/sess02_event_onset.csv']
'/home/username/MIA_projects/data/downloaded_data/sess02_event_onset.csv']

- *design_type* (a list of string which are bloc or event-related):
The type of design for each session (bloc design or event-related design).
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@@ -0,0 +1,66 @@
:orphan:

.. toctree::

+-----------------------------+-------------------------------------------+----------------------------------------------------+
|`Home <../../../index.html>`_|`Documentation <../../documentation.html>`_|`GitHub <https://github.com/populse/mia_processes>`_|
+-----------------------------+-------------------------------------------+----------------------------------------------------+

=============================
Get_Regressors_From_csv brick
=============================


Get regressors information (regressors names, values and session) for `Level1Design <../../bricks/stats/spm/Level1Design.html>`_ brick using csv files.
One csv file should be used by session.

The csv file should contains one column by regressor to add and the first row should contains the name of the regressor:

.. image:: ../../images/getRegressorsFromCSV_example.png
:width: 300
:alt: csv example event-related design

-----------------------------------------------


**Inputs parameters:**

- *csv_files* (a list of existing csv files):
csv files contening the regressors (one column by regressors),"
One csv file by session.

::

ex. ['/home/username/MIA_projects/data/downloaded_data/sess01_regressor.csv',
'/home/username/MIA_projects/data/downloaded_data/sess02_regressor.csv']


**Outputs parameters:**

- *sess_regress_level1design* (a list of items which are a list of items which are a dictionary with keys which are ‘name’ or ‘val’ and with values which are a string or a list of float):
Additional columns to include in the design matrix (sess_regress paremeter of the Level1Design brick)

::

ex. [
[
{
'name': 'reg1',
'val': [0.79, 0.98, 0.585, 0.805, 0.53, 1.155, 0.66, 1.14, 0.195, 1.045, 0.82, 0.49, 0.765, 0.67, 0.0, 0.12, 0.955, 0.935, 0.26, 0.865]
},
{
'name': 'reg2',
'val': [1.58, 1.96, 1.17, 1.61, 1.06, 2.31, 1.32, 2.28, 0.39, 2.09, 1.64, 0.98, 1.53, 1.34, 0.0, 0.24, 1.91, 1.87, 0.52, 1.73]
}
],
[
{
'name': 'reg1',
'val': [0.99, 0.563, 0.596, 0.752, 0.42, 1.2, 0.79, 1.3, 0.168, 1.12, 0.75, 0.99, 0.77, 0.23, 0.07, 0.63, 0.85, 0.75, 0.63, 0.44]
},
{
'name': 'reg2',
'val': [1.56, 1.88, 1.46, 1.32, 1.55, 2.86, 1.23, 2.98, 0.75, 1.2, 1.63, 0.88, 1.96, 1.55, 0.09, 0.32, 1.8, 1.9, 0.45, 1.2]
}
]
]
1 change: 1 addition & 0 deletions docs/html/_sources/documentation/documentation.rst.txt
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Expand Up @@ -172,6 +172,7 @@ To use certain mia_processes bricks (atomic processes), `third-party softwares u
- `Get_Conditions_From_csv <bricks/tools/Get_Conditions_From_csv.html>`_
- `Get_Eprime_info_GE2REC <bricks/tools/Get_Eprime_info_GE2REC.html>`_
- `Get_Patient_Name <bricks/tools/Get_Patient_Name.html>`_
- `Get_Regressors_From_csv <bricks/tools/Get_Regressors_From_csv.html>`_
- `Import_Data <bricks/tools/Import_Data.html>`_
- `Input_Filter <bricks/tools/Input_Filter.html>`_
- `List_Duplicate <bricks/tools/List_Duplicate.html>`_
Expand Down
4 changes: 0 additions & 4 deletions docs/html/_static/basic.css
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Expand Up @@ -237,10 +237,6 @@ a.headerlink {
visibility: hidden;
}

a:visited {
color: #551A8B;
}

h1:hover > a.headerlink,
h2:hover > a.headerlink,
h3:hover > a.headerlink,
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5 changes: 3 additions & 2 deletions docs/html/_static/documentation_options.js
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@@ -1,5 +1,6 @@
const DOCUMENTATION_OPTIONS = {
VERSION: '2.6.1-dev+d3e43d68',
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
VERSION: '2.6.1-dev+aa446e49',
LANGUAGE: 'en',
COLLAPSE_INDEX: false,
BUILDER: 'html',
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2 changes: 1 addition & 1 deletion docs/html/_static/haiku.css
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Expand Up @@ -57,7 +57,7 @@ a:link {
a:visited {
font-weight: bold;
text-decoration: none;
color: #551a8b;
color: #892601;
}

a:hover, a:active {
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Expand Up @@ -16,7 +16,6 @@ span.linenos.special { color: #000000; background-color: #ffffc0; padding-left:
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.highlight .gi { color: #00aa00 } /* Generic.Inserted */
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26 changes: 9 additions & 17 deletions docs/html/_static/searchtools.js
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Expand Up @@ -57,12 +57,12 @@ const _removeChildren = (element) => {
const _escapeRegExp = (string) =>
string.replace(/[.*+\-?^${}()|[\]\\]/g, "\\$&"); // $& means the whole matched string

const _displayItem = (item, searchTerms, highlightTerms) => {
const _displayItem = (item, searchTerms) => {
const docBuilder = DOCUMENTATION_OPTIONS.BUILDER;
const docUrlRoot = DOCUMENTATION_OPTIONS.URL_ROOT;
const docFileSuffix = DOCUMENTATION_OPTIONS.FILE_SUFFIX;
const docLinkSuffix = DOCUMENTATION_OPTIONS.LINK_SUFFIX;
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;

const [docName, title, anchor, descr, score, _filename] = item;

Expand All @@ -75,24 +75,20 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
if (dirname.match(/\/index\/$/))
dirname = dirname.substring(0, dirname.length - 6);
else if (dirname === "index/") dirname = "";
requestUrl = contentRoot + dirname;
requestUrl = docUrlRoot + dirname;
linkUrl = requestUrl;
} else {
// normal html builders
requestUrl = contentRoot + docName + docFileSuffix;
requestUrl = docUrlRoot + docName + docFileSuffix;
linkUrl = docName + docLinkSuffix;
}
let linkEl = listItem.appendChild(document.createElement("a"));
linkEl.href = linkUrl + anchor;
linkEl.dataset.score = score;
linkEl.innerHTML = title;
if (descr) {
if (descr)
listItem.appendChild(document.createElement("span")).innerHTML =
" (" + descr + ")";
// highlight search terms in the description
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
}
else if (showSearchSummary)
fetch(requestUrl)
.then((responseData) => responseData.text())
Expand All @@ -101,9 +97,6 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
listItem.appendChild(
Search.makeSearchSummary(data, searchTerms)
);
// highlight search terms in the summary
if (SPHINX_HIGHLIGHT_ENABLED) // set in sphinx_highlight.js
highlightTerms.forEach((term) => _highlightText(listItem, term, "highlighted"));
});
Search.output.appendChild(listItem);
};
Expand All @@ -122,15 +115,14 @@ const _finishSearch = (resultCount) => {
const _displayNextItem = (
results,
resultCount,
searchTerms,
highlightTerms,
searchTerms
) => {
// results left, load the summary and display it
// this is intended to be dynamic (don't sub resultsCount)
if (results.length) {
_displayItem(results.pop(), searchTerms, highlightTerms);
_displayItem(results.pop(), searchTerms);
setTimeout(
() => _displayNextItem(results, resultCount, searchTerms, highlightTerms),
() => _displayNextItem(results, resultCount, searchTerms),
5
);
}
Expand Down Expand Up @@ -368,7 +360,7 @@ const Search = {
// console.info("search results:", Search.lastresults);

// print the results
_displayNextItem(results, results.length, searchTerms, highlightTerms);
_displayNextItem(results, results.length, searchTerms);
},

/**
Expand Down
16 changes: 3 additions & 13 deletions docs/html/_static/sphinx_highlight.js
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Expand Up @@ -29,19 +29,14 @@ const _highlight = (node, addItems, text, className) => {
}

span.appendChild(document.createTextNode(val.substr(pos, text.length)));
const rest = document.createTextNode(val.substr(pos + text.length));
parent.insertBefore(
span,
parent.insertBefore(
rest,
document.createTextNode(val.substr(pos + text.length)),
node.nextSibling
)
);
node.nodeValue = val.substr(0, pos);
/* There may be more occurrences of search term in this node. So call this
* function recursively on the remaining fragment.
*/
_highlight(rest, addItems, text, className);

if (isInSVG) {
const rect = document.createElementNS(
Expand Down Expand Up @@ -145,10 +140,5 @@ const SphinxHighlight = {
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};

_ready(() => {
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* It will highlight words from the *previous* search query.
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if (typeof Search === "undefined") SphinxHighlight.highlightSearchWords();
SphinxHighlight.initEscapeListener();
});
_ready(SphinxHighlight.highlightSearchWords);
_ready(SphinxHighlight.initEscapeListener);
20 changes: 10 additions & 10 deletions docs/html/documentation/bricks/preprocess/afni/Automask.html
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@@ -1,21 +1,21 @@
<!DOCTYPE html>

<html lang="en" data-content_root="../../../../">
<html lang="en">
<head>
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" /><meta name="viewport" content="width=device-width, initial-scale=1" />

<title>Automask brick &#8212; mia_processes 2.6.1-dev+d3e43d68 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=f63d8bfa" />
<link rel="stylesheet" type="text/css" href="../../../../_static/haiku.css?v=e491ac2d" />
<script src="../../../../_static/documentation_options.js?v=717c3d5b"></script>
<title>Automask brick &#8212; mia_processes 2.6.1-dev+aa446e49 documentation</title>
<link rel="stylesheet" type="text/css" href="../../../../_static/pygments.css?v=659b1fac" />
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<script src="../../../../_static/sphinx_highlight.js?v=dc90522c"></script>
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<h2 class="heading"><span>Automask brick</span></h2>
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Expand All @@ -39,9 +39,9 @@ <h2 class="heading"><span>Automask brick</span></h2>
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<h1>Automask brick<a class="headerlink" href="#automask-brick" title="Link to this heading"></a></h1>
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<section id="create-a-brain-only-mask-of-the-image-using-afni-3dautomask">
<h2>Create a brain-only mask of the image using AFNI 3dAutomask<a class="headerlink" href="#create-a-brain-only-mask-of-the-image-using-afni-3dautomask" title="Link to this heading"></a></h2>
<h2>Create a brain-only mask of the image using AFNI 3dAutomask<a class="headerlink" href="#create-a-brain-only-mask-of-the-image-using-afni-3dautomask" title="Permalink to this heading"></a></h2>
<p>AFNI 3dClipLevel algorithm is used to find clipping level and after an erosion/dilation step, only the largest connected component of the supra-threshold voxels are kept.</p>
<p>Be carreful this program by itself does NOT do ‘skull-stripping’.</p>
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<h2 class="heading"><span>Calc brick</span></h2>
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Expand All @@ -39,9 +39,9 @@ <h2 class="heading"><span>Calc brick</span></h2>
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<section id="voxel-by-voxel-arithmetic-on-3d-datasets-using-afni-3dcalc">
<h2>Voxel-by-voxel arithmetic on <strong>3D datasets</strong> <a class="footnote-reference brackets" href="#label" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a>, using AFNI 3dcalc<a class="headerlink" href="#voxel-by-voxel-arithmetic-on-3d-datasets-using-afni-3dcalc" title="Link to this heading"></a></h2>
<h2>Voxel-by-voxel arithmetic on <strong>3D datasets</strong> <a class="footnote-reference brackets" href="#label" id="id1" role="doc-noteref"><span class="fn-bracket">[</span>1<span class="fn-bracket">]</span></a>, using AFNI 3dcalc<a class="headerlink" href="#voxel-by-voxel-arithmetic-on-3d-datasets-using-afni-3dcalc" title="Permalink to this heading"></a></h2>
<p>This bricks assumes that the voxel-by-voxel computations are being performed on datasets that occupy the same space and have the same orientations.</p>
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<p><strong>Mandatory inputs parameters:</strong></p>
Expand Down Expand Up @@ -176,7 +176,7 @@ <h2>Voxel-by-voxel arithmetic on <strong>3D datasets</strong> <a class="footnote

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