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Copy file name to clipboardExpand all lines: docs/user/_sources/subject_list_config.txt
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@@ -34,12 +34,13 @@ An example of such a YAML file can be found `here <https://raw.githubusercontent
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| | A value of 'None' means all sites will be run. This list can also be read from a text file. | file with site IDs separated by new lines, or 'None'. |
| scanParametersCSV | Path to a CSV specifying the slice time acquisition parameters for scans. If set to 'None', the NifTI headers will be used. | A path or 'None'. |
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| | Instructions for creating such a file can be found :doc:`here </func>`. | |
When you are done setting up the data configuration file, navigate in a terminal to the directory where you would like to store your subject list. Then, open iPython by typing :file:`ipython` and run one of the following commands from the iPython prompt.
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.. figure:: /_images/main_gui.png
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Now, to generate a subject list file, click on the *New* button next to the *Subject Lists* box. This will bring up the following dialog window:
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Now, to generate a subject list file, click on the *New* button next to the *Subject Lists* box. This will bring up the following dialog window, which will allow you to define the parameters of the data configuration YAML:
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.. figure:: /_images/subject_list_gui.png
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Each of the options in this window will now be described in the sections below.
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#. **Anatomical File Path Template - [text]:** A file path template for anatomical scans (see below for how to define templates).
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#. **Functional File Path Template - [text]:** A file path template for functional scans (see below for how to define templates).
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#. **Subjects to Include (Optional) - [text/path]:** An optional comma-separated list of subjects to include (if you wish to include only a subset of subjects whose scans match the templates). A value of 'None' means all subjects will be run. This list can also be read from a text file whose path is given in this field.
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#. **Subjects to Exclude (Optional) - [text/path]:** An optional comma-separated list of subjects to exclude (if you wish to exclude only a subset of subjects whose scans match the templates). A value of 'None' means all subjects will be run. This list can also be read from a text file whose path is given in this field.
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#. **Sites to Include (Optional) - [text/path]:** An optional comma-separated list of sites to include (if you wish to include only a subset of sites whose scans match the templates). A value of 'None' means all sites will be run. This list can also be read from a text file whose path is given in this field.
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#. **Scan Parameters File (Optional) - [path]:** Path to a CSV specifying the slice time acquisition parameters for scans. If set to 'None', the NifTI headers will be used. Instructions for creating such a file can be found :doc:`here </func>`.
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#. **Output Directory - [path]:** The directory where the subject list will be generated.
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#. **Subject List Name - [text]:** A name for the subject list.
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#. **Multiscan Data [checkbox]:** Check this box only if the scans have different slice timing information.
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Defining Anatomical and Functional File Path Templates
It should be noted that C-PAC currently requires subject directories to be within a site level directory. If your data set does not contain scans from multiple acquisition sites, we recommend creating a dummy :file:`site_1` directory and placing subject files inside this directory. This peculiarity will be fixed in future versions of C-PAC.
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As an example of how the templates work, the image below illustrates the file structure used by the `1000 Functional Connectomes <http://fcon_1000.projects.nitrc.org/fcpClassic/FcpTable.html>`_ data release and the resulting file path templates.
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.. figure:: /_images/nki-rs_template.png
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If you experience difficulties defining file path templates, you may want to re-organize your data to match one of the examples above. If you manually define a file path template and encounter an error when attempting to generate subject lists, please :doc:`contact us </help>` and we will be happy to help.
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Selectively Include or Exclude Subjects
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By default, C-PAC will process data for all subjects matching the file templates defined above. In many cases however, you may want to run only a subset of the subjects within a particular data set. In others, you may want to exclude particular subjects from analysis. This can be done by specifying a list of subjects through the :file:`subjectList` or :file:`exclusionSubjectList` options. Lists can be specified either as a text file or directly in :file:`data_config.yml`. Text files should contain one subject ID per line, with each subject ID matching the name of a subject folder. The same steps can used with the :file:`siteList` option to selectively process data from specific acquisition sites.
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Set Up Slice Timing Correction
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------------------------------
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If you wish to run :doc:`Slice Timing Correction </func>`, you must specify the path to a spreadsheet file containing scan acquisition parameters and slice timing information. Instructions for creating this file can be :doc:`found here </func>`, and we provide preconfigured versions for INDI data releases on the :doc:`Preconfigured Files </files>` page. If you do not wish to run Slice Timing Correction, set :file:`scanParametersCSV = None`.
<h3>Configuration Without the GUI<aclass="headerlink" href="#configuration-without-the-gui" title="Permalink to this headline">¶</a></h3>
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<p>The following key/value pairs must be defined in your <aclass="reference internal" href="pipeline_config.html"><em>pipeline configuration YAML</em></a> for C-PAC to run anatomical preprocessing:</p>
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<blockquote>
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<div><tableborder="1" class="docutils">
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<colgroup>
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<colwidth="13%" />
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<colwidth="52%" />
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<colwidth="35%" />
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</colgroup>
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<theadvalign="bottom">
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<trclass="row-odd"><thclass="head">Key</th>
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<thclass="head">Description</th>
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<thclass="head">Potential Values</th>
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</tr>
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</thead>
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<tbodyvalign="top">
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<trclass="row-even"><td>runALFF</td>
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<td>Calculate Amplitude of Low Frequency Fluctuations (ALFF) and and fractional ALFF (f/ALFF) for all voxels.</td>
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<td>A list where ‘1’ represents ‘yes’ and ‘0’ represents ‘no’ (e.g., ‘[1]’).</td>
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</tr>
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<trclass="row-odd"><td>highPassFreqALFF</td>
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<td>Frequency cutoff (in Hz) for the high-pass filter used when calculating f/ALFF.</td>
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<td>A list containing a decimal value (e.g., ‘[0.01]’).</td>
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</tr>
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<trclass="row-even"><td>lowPassFreqALFF</td>
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<td>Frequency cutoff (in Hz) for the low-pass filter used when calculating f/ALFF.</td>
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<td>A list containing a decimal value (e.g., ‘[0.1]’).</td>
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</tr>
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</tbody>
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</table>
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</div></blockquote>
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</div>
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</div>
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<divclass="section" id="references">
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<h3><ahref="index.html">Table Of Contents</a></h3>
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