skimage packages for the core functionality, plus the matplotlib, pandas, and transform3d packages for some optional functions and modules. See the requirements.txt file for a complete list.
+Required packages include (among others) the nibabel and skimage packages for the core functionality, plus the matplotlib, pandas, and transform3d packages for some optional functions and modules. See the requirements.txt file for a complete list.
Use the following command to install these packages:
`
bash
@@ -281,7 +281,7 @@ Requirements`
If installing the toolbox as a Python package or if using the Docker image, all required packages will be installed automatically, and manual installation as detailed above will not be necessary.
This software has been tested on Ubuntu 20.04.
This software has been tested on Ubuntu 20.04 and Ubuntu 22.04.
A working FreeSurfer installation (version 6 or newer) is required for running the ‘shape’ module of this toolbox. Also, make sure that FreeSurfer is sourced (i.e., FREESURFER_HOME is set as an environment variable) before running an analysis.
run_fsqc
--subjects_dir <directory>
--output_dir <directory>
-[--subjects SubjectID]
+[--subjects SubjectID [SubjectID ...]]
[--subjects-file <file>] [--screenshots]
[--screenshots-html] [--surfaces] [--surfaces-html]
[--skullstrip] [--skullstrip-html]
[--fornix] [--fornix-html] [--hippocampus]
[--hippocampus-html] [--hippocampus-label ... ]
[--hypothalamus] [--hypothalamus-html] [--shape]
-[--outlier] [--fastsurfer] [-h] [--more-help]
+[--outlier] [--fastsurfer] [--no-group]
+[--group-only] [--exit-on-error]
+[--skip-existing] [-h] [--more-help]
[...]
Required Arguments:
@@ -354,9 +356,18 @@ As a Command Line Tool Use FastSurfer instead of FreeSurfer output
+--no-group
+ run script in subject-level mode. will compute individual files and statistics, but not create group-level summaries.
+
+--group-only
+ run script in group mode. will create group-level summaries from existing inputs. needs to be run on output directory with already existing results.
+
--exit-on-error
Terminate the program when encountering an error; otherwise, try to continue with the next module or case
+--skip-existing
+ skips processing for a given case if output already exists, even with possibly different parameters or settings
+
Getting Help:
-------------
-h, --help
@@ -546,7 +557,7 @@ As a Docker Image
-
+
diff --git a/dev/_sources/Requirements.rst.txt b/dev/_sources/Requirements.rst.txt
index f285f2a..8ce08a8 100644
--- a/dev/_sources/Requirements.rst.txt
+++ b/dev/_sources/Requirements.rst.txt
@@ -14,7 +14,7 @@ Requirements
```
- If installing the toolbox as a Python package or if using the Docker image, all required packages will be installed automatically, and manual installation as detailed above will not be necessary.
-- This software has been tested on Ubuntu 20.04.
+- This software has been tested on Ubuntu 20.04 and Ubuntu 22.04.
- A working `FreeSurfer
+ run_fsqc
+ --subjects_dir
--output_dir
- [--subjects SubjectID]
+ [--subjects SubjectID [SubjectID ...]]
[--subjects-file ] [--screenshots]
[--screenshots-html] [--surfaces] [--surfaces-html]
[--skullstrip] [--skullstrip-html]
[--fornix] [--fornix-html] [--hippocampus]
[--hippocampus-html] [--hippocampus-label ... ]
[--hypothalamus] [--hypothalamus-html] [--shape]
- [--outlier] [--fastsurfer] [-h] [--more-help]
+ [--outlier] [--fastsurfer] [--no-group]
+ [--group-only] [--exit-on-error]
+ [--skip-existing] [-h] [--more-help]
[...]
Required Arguments:
-------------------
--subjects_dir
- Subjects directory with a set of Freesurfer- or
+ Subjects directory with a set of Freesurfer- or
Fastsurfer-processed individual datasets.
--output_dir
@@ -88,9 +90,18 @@ As a Command Line Tool
--fastsurfer
Use FastSurfer instead of FreeSurfer output
+ --no-group
+ run script in subject-level mode. will compute individual files and statistics, but not create group-level summaries.
+
+ --group-only
+ run script in group mode. will create group-level summaries from existing inputs. needs to be run on output directory with already existing results.
+
--exit-on-error
Terminate the program when encountering an error; otherwise, try to continue with the next module or case
+ --skip-existing
+ skips processing for a given case if output already exists, even with possibly different parameters or settings
+
Getting Help:
-------------
-h, --help
@@ -102,34 +113,34 @@ As a Command Line Tool
---------------
--screenshots_base
Filename of an image that should be used instead of
- norm.mgz as the base image for the screenshots. Can be
- an individual file (which would not be appropriate for
- multi-subject analysis) or can be a file without
+ norm.mgz as the base image for the screenshots. Can be
+ an individual file (which would not be appropriate for
+ multi-subject analysis) or can be a file without
pathname and with the same filename across subjects within the 'mri'
- subdirectory of an individual FreeSurfer results directory
+ subdirectory of an individual FreeSurfer results directory
(which would be appropriate for multi-subject analysis).
--screenshots_overlay
- Path to an image that should be used instead of aseg.mgz
- as the overlay image for the screenshots can also be none.
- Can be an individual file (which would not be appropriate
+ Path to an image that should be used instead of aseg.mgz
+ as the overlay image for the screenshots can also be none.
+ Can be an individual file (which would not be appropriate
for multi-subject analysis) or can be a file without pathname
and with the same filename across subjects within the 'mri' subdirectory
- of an individual FreeSurfer results directory
+ of an individual FreeSurfer results directory
(which would be appropriate for multi-subject analysis).
--screenshots_surf [ ...]
- One or more surface files that should be used instead of
+ One or more surface files that should be used instead of
[lr]h.white and [lr]h.pial; can also be none.
- Can be one or more individual file(s) (which would not
+ Can be one or more individual file(s) (which would not
be appropriate for multi-subject analysis) or
- can be a (list of) file(s) without pathname and with the same
+ can be a (list of) file(s) without pathname and with the same
filename across subjects within the 'surf'
- subdirectory of an individual FreeSurfer results directory
+ subdirectory of an individual FreeSurfer results directory
(which would be appropriate for multi-subject analysis).
--screenshots_views [ ...]
- One or more views to use for the screenshots in the form of
+ One or more views to use for the screenshots in the form of
x= y= and/or z=.
Order does not matter. Default views are x=-10 x=10 y=0 z=0.
diff --git a/dev/_static/basic.css b/dev/_static/basic.css
index f316efc..7ebbd6d 100644
--- a/dev/_static/basic.css
+++ b/dev/_static/basic.css
@@ -1,12 +1,5 @@
/*
- * basic.css
- * ~~~~~~~~~
- *
* Sphinx stylesheet -- basic theme.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
/* -- main layout ----------------------------------------------------------- */
@@ -115,15 +108,11 @@ img {
/* -- search page ----------------------------------------------------------- */
ul.search {
- margin: 10px 0 0 20px;
- padding: 0;
+ margin-top: 10px;
}
ul.search li {
- padding: 5px 0 5px 20px;
- background-image: url(file.png);
- background-repeat: no-repeat;
- background-position: 0 7px;
+ padding: 5px 0;
}
ul.search li a {
diff --git a/dev/_static/doctools.js b/dev/_static/doctools.js
index 4d67807..0398ebb 100644
--- a/dev/_static/doctools.js
+++ b/dev/_static/doctools.js
@@ -1,12 +1,5 @@
/*
- * doctools.js
- * ~~~~~~~~~~~
- *
* Base JavaScript utilities for all Sphinx HTML documentation.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
"use strict";
diff --git a/dev/_static/language_data.js b/dev/_static/language_data.js
index 367b8ed..c7fe6c6 100644
--- a/dev/_static/language_data.js
+++ b/dev/_static/language_data.js
@@ -1,13 +1,6 @@
/*
- * language_data.js
- * ~~~~~~~~~~~~~~~~
- *
* This script contains the language-specific data used by searchtools.js,
* namely the list of stopwords, stemmer, scorer and splitter.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
var stopwords = ["a", "and", "are", "as", "at", "be", "but", "by", "for", "if", "in", "into", "is", "it", "near", "no", "not", "of", "on", "or", "such", "that", "the", "their", "then", "there", "these", "they", "this", "to", "was", "will", "with"];
diff --git a/dev/_static/searchtools.js b/dev/_static/searchtools.js
index b08d58c..2c774d1 100644
--- a/dev/_static/searchtools.js
+++ b/dev/_static/searchtools.js
@@ -1,12 +1,5 @@
/*
- * searchtools.js
- * ~~~~~~~~~~~~~~~~
- *
* Sphinx JavaScript utilities for the full-text search.
- *
- * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
- * :license: BSD, see LICENSE for details.
- *
*/
"use strict";
@@ -20,7 +13,7 @@ if (typeof Scorer === "undefined") {
// and returns the new score.
/*
score: result => {
- const [docname, title, anchor, descr, score, filename] = result
+ const [docname, title, anchor, descr, score, filename, kind] = result
return score
},
*/
@@ -47,6 +40,14 @@ if (typeof Scorer === "undefined") {
};
}
+// Global search result kind enum, used by themes to style search results.
+class SearchResultKind {
+ static get index() { return "index"; }
+ static get object() { return "object"; }
+ static get text() { return "text"; }
+ static get title() { return "title"; }
+}
+
const _removeChildren = (element) => {
while (element && element.lastChild) element.removeChild(element.lastChild);
};
@@ -64,9 +65,13 @@ const _displayItem = (item, searchTerms, highlightTerms) => {
const showSearchSummary = DOCUMENTATION_OPTIONS.SHOW_SEARCH_SUMMARY;
const contentRoot = document.documentElement.dataset.content_root;
- const [docName, title, anchor, descr, score, _filename] = item;
+ const [docName, title, anchor, descr, score, _filename, kind] = item;
let listItem = document.createElement("li");
+ // Add a class representing the item's type:
+ // can be used by a theme's CSS selector for styling
+ // See SearchResultKind for the class names.
+ listItem.classList.add(`kind-${kind}`);
let requestUrl;
let linkUrl;
if (docBuilder === "dirhtml") {
@@ -115,8 +120,10 @@ const _finishSearch = (resultCount) => {
"Your search did not match any documents. Please make sure that all words are spelled correctly and that you've selected enough categories."
);
else
- Search.status.innerText = _(
- "Search finished, found ${resultCount} page(s) matching the search query."
+ Search.status.innerText = Documentation.ngettext(
+ "Search finished, found one page matching the search query.",
+ "Search finished, found ${resultCount} pages matching the search query.",
+ resultCount,
).replace('${resultCount}', resultCount);
};
const _displayNextItem = (
@@ -138,7 +145,7 @@ const _displayNextItem = (
else _finishSearch(resultCount);
};
// Helper function used by query() to order search results.
-// Each input is an array of [docname, title, anchor, descr, score, filename].
+// Each input is an array of [docname, title, anchor, descr, score, filename, kind].
// Order the results by score (in opposite order of appearance, since the
// `_displayNextItem` function uses pop() to retrieve items) and then alphabetically.
const _orderResultsByScoreThenName = (a, b) => {
@@ -248,6 +255,7 @@ const Search = {
searchSummary.classList.add("search-summary");
searchSummary.innerText = "";
const searchList = document.createElement("ul");
+ searchList.setAttribute("role", "list");
searchList.classList.add("search");
const out = document.getElementById("search-results");
@@ -318,7 +326,7 @@ const Search = {
const indexEntries = Search._index.indexentries;
// Collect multiple result groups to be sorted separately and then ordered.
- // Each is an array of [docname, title, anchor, descr, score, filename].
+ // Each is an array of [docname, title, anchor, descr, score, filename, kind].
const normalResults = [];
const nonMainIndexResults = [];
@@ -337,6 +345,7 @@ const Search = {
null,
score + boost,
filenames[file],
+ SearchResultKind.title,
]);
}
}
@@ -354,6 +363,7 @@ const Search = {
null,
score,
filenames[file],
+ SearchResultKind.index,
];
if (isMain) {
normalResults.push(result);
@@ -475,6 +485,7 @@ const Search = {
descr,
score,
filenames[match[0]],
+ SearchResultKind.object,
]);
};
Object.keys(objects).forEach((prefix) =>
@@ -585,6 +596,7 @@ const Search = {
null,
score,
filenames[file],
+ SearchResultKind.text,
]);
}
return results;
diff --git a/dev/api/generated/fsqc.checkCCSize.html b/dev/api/generated/fsqc.checkCCSize.html
index 15e3199..7046cea 100644
--- a/dev/api/generated/fsqc.checkCCSize.html
+++ b/dev/api/generated/fsqc.checkCCSize.html
@@ -5,7 +5,7 @@
-
+
fsqc.checkCCSize - fsqc
@@ -281,15 +281,15 @@
- Parameters:
-
- Returns:
-
@@ -375,7 +375,7 @@
floatSignal-to-noise ratio (SNR) for the left hemisphere WM/GM contrast.
+floatSignal-to-noise ratio (SNR) for the left hemisphere WM/GM contrast.
floatSignal-to-noise ratio (SNR) for the right hemisphere WM/GM contrast.
+floatSignal-to-noise ratio (SNR) for the right hemisphere WM/GM contrast.
floatRotation angle around the x-axis in radians.
+floatRotation angle around the x-axis in radians.
floatRotation angle around the y-axis in radians.
+floatRotation angle around the y-axis in radians.
floatRotation angle around the z-axis in radians.
+floatRotation angle around the z-axis in radians.
strThe directory containing subject data.
+strThe directory containing subject data.
strThe name of the subject.
+strThe name of the subject.
int, optionalThe number of erosions, default is 3.
+int, optionalThe number of erosions, default is 3.
str, optionalThe reference image, default is “norm.mgz”, can be changed to “orig.mgz”.
+str, optionalThe reference image, default is “norm.mgz”, can be changed to “orig.mgz”.
str, optionalThe aparc+aseg image, default is “aparc+aseg.mgz”, can +
str, optionalThe aparc+aseg image, default is “aparc+aseg.mgz”, can be changed to “aparc+aseg.orig.mgz” for FastSurfer output.
intNumber of holes in the left hemisphere.
+intNumber of holes in the left hemisphere.
intNumber of holes in the right hemisphere.
+intNumber of holes in the right hemisphere.
intNumber of defects in the left hemisphere.
+intNumber of defects in the left hemisphere.
intNumber of defects in the right hemisphere.
+intNumber of defects in the right hemisphere.
floatTopological fixing time for the left hemisphere.
+floatTopological fixing time for the left hemisphere.
floatTopological fixing time for the right hemisphere.
+floatTopological fixing time for the right hemisphere.
This module provides a function to create screenshots
Function to create screenshots.
strThe subject.
+strThe subject.
strThe subjects directory.
+strThe subjects directory.
strThe output file path.
+strThe output file path.
bool, optionalFlag for interactive mode, default is True.
+bool, optionalFlag for interactive mode, default is True.
str, optionalThe layout, default is None.
+list, optionalThe layout, default is “default”.
list, optionalThe base, default is [“default”].
+str, optionalThe base, default is “default”. +Load norm.mgz as default.
list, optionalThe overlay, default is [“default”].
+str, optionalThe overlay, default is “default”. +Load aseg.mgz as default. +Can be None.
None or str, optionalThe labels, default is None.
+None or str, optionalThe labels, default is None.
list, optionalThe surface, default is [“default”].
+list, optionalThe surface, default is “default”. +Can be None.
list, optionalThe surface color, default is [“default”].
+list, optionalThe surface color, default is “default”. +Can be None.
list, optionalThe views, default is [“default”].
+list, optionalThe views, default is “default”.
None or list, optionalThe x limits, default is None.
+None or list, optionalThe x limits, default is None.
None or list, optionalThe y limits, default is None.
+None or list, optionalThe y limits, default is None.
bool, optionalFlag for binarization, default is False.
+bool, optionalFlag for binarization, default is False.
list, optionalThe orientation, default is [“radiological”].
+str, optionalThe orientation, default is “radiological”.
Notes
-BASE, VIEWS must be lists, can be [“default”].
-OVERLAY, SURF, SURFCOLOR can be lists or None, can be [“default”].
+LAYOUT, VIEWS can be lists or “default”.
+SURF, SURFCOLOR can be lists, None, or “default”.
XLIM, YLIM can be lists of list two-element numeric lists or None; if given, length must match length of VIEWS. x and y refer to final image dimensions, not MR volume dimensions.
@@ -396,7 +401,7 @@ - + diff --git a/dev/api/generated/fsqc.createSurfacePlots.html b/dev/api/generated/fsqc.createSurfacePlots.html index 5e4069a..bccde31 100644 --- a/dev/api/generated/fsqc.createSurfacePlots.html +++ b/dev/api/generated/fsqc.createSurfacePlots.html @@ -5,7 +5,7 @@ - +strThe subject.
+strThe subject.
strThe subjects directory.
+strThe subjects directory.
strThe output directory for surface plots.
+strThe output directory for surface plots.
listList of views for which surface plots should be created.
+listList of views for which surface plots should be created.
boolFlag indicating whether FastSurfer processing was used.
+boolFlag indicating whether FastSurfer processing was used.
This module provides a function to evaluate potential missegmentation of the fornix
Evaluate potential missegmentation of the fornix.
This script assesses the potential missegmentation of the fornix, which might erroneously be attached to the ‘corpus callosum’ label.
@@ -288,19 +288,21 @@strThe subject identifier.
+strThe subject identifier.
strThe directory containing subject data.
+strThe directory containing subject data.
strThe output directory.
+strThe output directory.
bool, optional (default: True)Whether to create screenshots.
+bool, optional (default: True)Whether to create screenshots.
str or list, optional (default: [])File or list of files for screenshots.
+str or list, optional (default: None)File or list of files for screenshots.
bool, optional (default: True)Whether to run shape analysis.
+bool, optional (default: True)Whether to run shape analysis.
int, optional (default: 30)Number of Eigenvalues for shape analysis.
+int, optional (default: 30)Number of Eigenvalues for shape analysis.
+bool, optional (default: True)Write csv file with eigenvalues (or nans) to output directory.
Evaluate potential missegmentation of the hippocampus and amygdala.
This script evaluates potential missegmentation of the hippocampus and amygdala as created by FreeSurfer 7.1’s dedicated module: @@ -285,27 +285,27 @@
strThe subject identifier.
+strThe subject identifier.
strThe directory containing subject data.
+strThe directory containing subject data.
strThe output directory.
+strThe output directory.
bool, optional, default: TrueWhether to create screenshots.
+bool, optional, default: TrueWhether to create screenshots.
str or list, optional, default: []File or list of files for screenshots.
+str or list, optional, default: NoneFile or list of files for screenshots.
str or list, optional, default: [“radiological”]Orientation or list of orientations for screenshots.
+str, optional, default: “radiological”Orientation for screenshots.
str, optional, default: “lh”Hemisphere to evaluate, either ‘lh’ or ‘rh’.
+str, optional, default: “lh”Hemisphere to evaluate, either ‘lh’ or ‘rh’.
str, optional, default: “T1.v21”Label for hippocampal and amygdala segmentation.
+str, optional, default: “T1.v21”Label for hippocampal and amygdala segmentation.
This module provides a function to evaluate potential missegmentation of the hypothalamus
Evaluate potential missegmentation of the hypothalamus.
This script evaluates potential missegmentation of the hypothalamus as created by FreeSurfer 7.2’s module for hypothalamic segmentation: @@ -284,23 +284,23 @@
strThe subject identifier.
+strThe subject identifier.
strThe directory containing subject data.
+strThe directory containing subject data.
strThe output directory.
+strThe output directory.
bool, optional, default: TrueWhether to create screenshots.
+bool, optional, default: TrueWhether to create screenshots.
str or list, optional, default: []File or list of files for screenshots.
+str or list, optional, default: NoneFile or list of files for screenshots.
str or list, optional, default: [“radiological”]Orientation or list of orientations for screenshots.
+str, optional, default: “radiological”Orientation for screenshots.
bool, optional, default: TrueWhether to print the help message.
+bool, optional, default: TrueWhether to print the help message.
bool, optional, default: FalseWhether to return the help message as a string.
+bool, optional, default: FalseWhether to return the help message as a string.
None or strIf print_help is True, the help message is printed. If return_help
+
None or strIf print_help is True, the help message is printed. If return_help
is True, the help message is returned as a string.
Run the fsqc submodules.
This is the main function to run the fsqc submodules.
strSubjects directory.
+strSubjects directory.
strOutput directory.
+strOutput directory.
dict, default: NoneDictionary of input arguments.
+dict, default: NoneDictionary of input arguments.
list of str, default: NoneList of subjects to process. If None, all valid cases in the input +
list of str, default: NoneList of subjects to process. If None, all valid cases in the input
directory will be processed. Cannot be used with subjects_file.
str, default: NoneA text file that contains a list of subjects to be processed. Cannot +
str, default: NoneA text file that contains a list of subjects to be processed. Cannot
be used with subjects.
bool, default: FalseConduct shape analysis using brainprint.
+bool, default: FalseConduct shape analysis using brainprint.
bool, default: FalseCreate screenshots of MR image with optional overlays.
+bool, default: FalseCreate screenshots of MR image with optional overlays.
bool, default: FalseCreate screenshots and html summary page.
+bool, default: FalseCreate screenshots and html summary page.
str, default: “default”Filename for base image for screenshots.
+str, default: “default”Filename for base image for screenshots.
str, default: “default”Filename for overlay image for screenshots.
+str, default: “default”Filename for overlay image for screenshots.
list of str, default: “default”List of filenames of surface files to include in screenshots.
+list of) str, default: “default”List of filenames of surface files to include in screenshots.
list of str, default: “default”List of parameters to set the views of the screenshots. +
list of) str, default: “default”List of parameters to set the views of the screenshots. Example: [‘x=0’, ‘x=-10’, ‘x=10’, ‘y=20’, ‘z=0’].
list of int, default: NoneLayout describing rows and columns of the screenshots. +
str or list of int, default: “default”Layout describing rows and columns of the screenshots. Example: [1, 4] (one row, four columns).
list of str, default: [“radiological”]Orientation of screenshots. Either “radiological” or “neurological”.
+str, default: “radiological”Orientation of screenshots. Either “radiological” or “neurological”.
bool, default: FalseCreate screenshots of pial and inflated surfaces.
+bool, default: FalseCreate screenshots of pial and inflated surfaces.
bool, default: FalseCreate screenshots of pial and inflated surfaces and html summary page.
+bool, default: FalseCreate screenshots of pial and inflated surfaces and html summary page.
list of str, default: [“left”, “right”, “superior”, “inferior”]List of parameters to set the views of the surface plots.
+list of str, default: [“left”, “right”, “superior”, “inferior”]List of parameters to set the views of the surface plots.
bool, default: FalseCreate screeenshot of MR image and skullstrip overlay.
+bool, default: FalseCreate screeenshot of MR image and skullstrip overlay.
bool, default: FalseCreate screeenshot of MR image and skullstrip overlay, and create html +
bool, default: FalseCreate screeenshot of MR image and skullstrip overlay, and create html summary page.
bool, default: FalseCreate screenshot of MR imge and corpus callosum overlay to identify +
bool, default: FalseCreate screenshot of MR imge and corpus callosum overlay to identify fornix oversegmentation.
bool, default: FalseCreate screenshot of MR imge and corpus callosum overlay with html +
bool, default: FalseCreate screenshot of MR imge and corpus callosum overlay with html summary page.
bool, default: FalseCreate screenhots of hypothalamic segmentation. Requires running +
bool, default: FalseCreate screenhots of hypothalamic segmentation. Requires running FreeSurfer’s hypothalamus add-on module.
bool, default: FalseCreate screenhots of hypothalamic segmentation with html summary page. +
bool, default: FalseCreate screenhots of hypothalamic segmentation with html summary page. Requires running FreeSurfer’s hypothalamus add-on module.
bool, default: FalseCreate screenhots of hippocampal segmentation. Requires running +
bool, default: FalseCreate screenhots of hippocampal segmentation. Requires running FreeSurfer’s hippocampus add-on module.
bool, default: FalseCreate screenhots of hippocampal segmentation with html summary page. +
bool, default: FalseCreate screenhots of hippocampal segmentation with html summary page. Requires running FreeSurfer’s hippocampus add-on module.
str, default: NoneLabel used for the hippocampal segmentations. Example: “T1.v21”. The +
str, default: NoneLabel used for the hippocampal segmentations. Example: “T1.v21”. The full filename would be [lr]h.hippoAmygLabels-<LABEL>.FSvoxelSpace.mgz.
bool, default: FalseConduct outlier analysis.
+bool, default: FalseConduct outlier analysis.
str, default: NoneSpecify custom norms table for outlier analysis.
+str, default: NoneSpecify custom norms table for outlier analysis.
bool, default: FalseUse FastSurfer instead of FreeSurfer input.
+bool, default: FalseUse FastSurfer instead of FreeSurfer input.
bool, default: FalseExit on error. If False, a warning is thrown and the analysis +
bool, default: FalseRun script in subject-level mode. will compute individual files and +statistics, but not create group-level summaries.
+bool, default: FalseRun script in group mode. will create group-level summaries from +existing inputs.
+bool, default: FalseExit on error. If False, a warning is thrown and the analysis continues.
str, default: NoneSpecify a custom location for the logfile. Default location is the +
bool, default: FalseSkip processing for a given case if output already exists, even with +possibly different parameters or settings.
+str, default: NoneSpecify a custom location for the logfile. Default location is the output directory.
strInput image file path.
+strInput image file path.
strOutput transformed image file path.
+strOutput transformed image file path.
strTransformation matrix file path (must be in xfm or lta format).
+strTransformation matrix file path (must be in xfm or lta format).
Interpolation method to use.
strPath to the input image file.
+strPath to the input image file.
strPath to save the binarized image.
+strPath to save the binarized image.
None, optionalValues to consider as True. If None, non-zero values are considered True.
+None, optionalValues to consider as True. If None, non-zero values are considered True.
numpy.ndarrayArray of values corresponding to vertex points, shape (n,).
list or numpy.ndarrayList or array of level set values.
+list or numpy.ndarrayList or array of level set values.
listList of interpolated vertices for each level set.
+listList of interpolated vertices for each level set.
listList of triangle indices corresponding to the interpolated vertices for each level set.
+listList of triangle indices corresponding to the interpolated vertices for each level set.
listList of triangle indices that intersect with the level set.
+listList of triangle indices that intersect with the level set.
dictA dictionary containing transformation information, including type, number of transforms, +
dictA dictionary containing transformation information, including type, number of transforms, mean, sigma, and transformation matrices for source and destination volumes.
listList of subject IDs.
+listList of subject IDs.
strPath to the FreeSurfer subjects directory.
+strPath to the FreeSurfer subjects directory.
strPath to the output directory for saving results.
+strPath to the output directory for saving results.
dictDictionary containing outlier thresholds for different measures.
+dictDictionary containing outlier thresholds for different measures.
int, optionalMinimum number of subjects required for analysis.
+int, optionalMinimum number of subjects required for analysis.
bool, optionalFlag to include hypothalamic values in the analysis.
+bool, optionalFlag to include hypothalamic values in the analysis.
bool, optionalFlag to include hippocampal values in the analysis.
+bool, optionalFlag to include hippocampal values in the analysis.
str or None, optionalLabel to identify the hippocampus (e.g., “Hippocampus”).
+str or None, optionalLabel to identify the hippocampus (e.g., “Hippocampus”).
bool, optionalFlag to use FastSurfer instead of FreeSurfer output files.
+bool, optionalFlag to use FastSurfer instead of FreeSurfer output files.
tupleA tuple containing three dictionaries:
+tupleA tuple containing three dictionaries:
outlierSampleNonparNum
outlierSampleParamNum
tupleA tuple containing three dictionaries:
+tupleA tuple containing three dictionaries:
Header information for the aparc.stats file.
Detailed measures for different anatomical regions.