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        <title>LNCD</title>
        <link>https://lncd.pitt.edu/wiki/</link>
        <url>https://lncd.pitt.edu/wiki/lib/exe/fetch.php?media=wiki:dokuwiki.svg</url>
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        <dc:date>2026-04-04T00:19:56+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>SPA MR - [SPA MR] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:spa:mr&amp;rev=1775261996&amp;do=diff</link>
        <description>SPA MR

Synaptic Pruning Adolescence (SPA) MRI acquisitions on BST3 7TPlus

Also see

	*  Table Change
	*  [WPC-8922 sTx/P31 MR protocol PDF] (“Phoenix report”)
	*  SPA 7T Scanner DICOM files

pTx

	*  MRSI using MRSI Slice Positioning tool (QPASA) (PFC ROI Placement)
	*  dwi
	*  Switch Task at 7T (green=127s, red=138s, longmix1, longmix2 = 425s)
	*  Resting State Task x2 (before/after task; eyes open, no fix cross, see black screen powerpoint slide)</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-03-25T20:00:17+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>AFNI GUI</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:afni_gui&amp;rev=1774468817&amp;do=diff</link>
        <description>AFNI GUI

AFNI&#039;s Graphical User Interface has a deep feature set.

Slider

You can slide between overlay and underlay. Enable this mode by pushing 3 or 4 with an image window focused.

Graph View

For underlays with a time dimension (multiple values), the</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-03-25T19:58:06+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>7T MR Quality Check - [T1w Warps] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:7t:mr:qc&amp;rev=1774468686&amp;do=diff</link>
        <description>7T MR Quality Check

T1w Warps

	*  annotations: &lt;https://pitt-my.sharepoint.com/:x:/g/personal/foran_pitt_edu/Ef-YdXhtcUVGsi0go0i1JoMBdPGYgzq1_z3Y5Y8wfvsVkQ?e=uyr3bl&gt;
	*  concatenated visit-per-volume (via LNCD Tools&#039;s 4dConcatSubBrik  ) T1w skull strips warped to mni for (all) original, mp2rage denoised (via Val!), and only mprage (7T_brainwarp_40mprage-only.nii.gz) 
	*  ideal for</description>
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    <item rdf:about="https://lncd.pitt.edu/wiki/doku.php?id=tools:preprocessfunctional&amp;rev=1774468656&amp;do=diff">
        <dc:format>text/html</dc:format>
        <dc:date>2026-03-25T19:57:36+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>Preprocess Functional (Hallquist pipeline) - [QC] </title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:preprocessfunctional&amp;rev=1774468656&amp;do=diff</link>
        <description>Preprocess Functional (Hallquist pipeline)

	*  &lt;https://github.com/LabNeuroCogDevel/fmri_processing_scripts&gt;
	*  &lt;https://zenodo.org/badge/latestdoi/5274327&gt;

Developed by Michael Hallquist

Output 4D nifti prefix

As the pipeline progresses it outputs files with distinct prefixes that describe each step in reverse order. e.g. final output might be brnwsdktm_func_4.nii.gz</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-03-25T19:27:56+00:00</dc:date>
        <dc:creator>will (will@undisclosed.example.com)</dc:creator>
        <title>AFNI</title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=tools:afni&amp;rev=1774466876&amp;do=diff</link>
        <description>AFNI

Also see the AFNI GUI subpage for tips on the graphical interface.

DataTable

3dMVM and 3dLME can take an input table like 3dMVM ... -dataTable @myfile.tsv. Both are very particular about the format of the input file.

	*  Subj must be the name of the first column (and thus the first word of the file)</description>
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        <dc:format>text/html</dc:format>
        <dc:date>2026-03-23T16:33:57+00:00</dc:date>
        <dc:creator>creelyhn (creelyhn@undisclosed.example.com)</dc:creator>
        <title></title>
        <link>https://lncd.pitt.edu/wiki/doku.php?id=grants:spa:spa-pet&amp;rev=1774283637&amp;do=diff</link>
        <description>PRIMARY CONTACTS:

	*  Mara and Michael – coordinators: mac613@pitt.edu  AND  himesml2@upmc.edu
	*  James – Manager (if there’s ever a question, he’s your guy!): ruszkiewiczja@upmc.edu
	*  Dr. Raj – MD always on call when participant is here: ran29@pitt.edu</description>
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        <title>fmriprep - [Considerations] </title>
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        <description>fmriprep

Find full documentation on &lt;https://fmriprep.org/en/stable/&gt;

Also see fMRI Preprocessing, Preprocess Functional (Hallquist pipeline)

Follow up fmriprep outputs (*_desc-preproc_bold.nii.gz) with xcpd.

Example usage:

	*  Hera/Projects/Habit/mr/fmriprep_habitstudy.bash

Considerations

	*  fmriprep can reuse freesurfer when run before (otherwise will run minimal version internally).</description>
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        <title>fMRI Preprocessing</title>
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        <description>fMRI Preprocessing

This page is a generic overview. For specific software see

	*  fmriprep + xcpd -- BIDS App standard functional MRI preprocessing
	*  Preprocess Functional (Hallquist pipeline) -- in-house legacy pipeline from Hallquist. Has useful features and exists for older studies (Cog Grant, PET Study, Brain Mechanisms R01 (7T))

Considerations:</description>
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        <description>Synaptic Pruning Adolescence (SPA)

	*  R01MH067924: &lt;https://reporter.nih.gov/project-details/10653380&gt;
	*  National Data Archive collection 4840: &lt;https://nda.nih.gov/edit_collection.html?id=4840&gt;
	*  behavioral protocol
	*  SPA MR
	*  SPA EEG
	*  SPA-PET</description>
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