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FsTutorial/Scripts . . . 11 matches
...<<TableOfContents>> == FreeSurfer Scripts == === Aliases === If you find yourself typing the same commands over and over, a nice shortcut is to make an alias for it. An alias is a...

11.4k - rev: 19 (current) last modified: 2016-11-04 17:13:29

DevelopersGuide/QtDevelopersGuide . . . 11 matches
...ents(4)>> This page is targeted at those who want to develop Qt applications in the FreeSurfer code tree. === Usual Workflow of Qt Developers === If you are new to Qt programmi...

12.9k - rev: 9 (current) last modified: 2012-02-06 19:13:48

CorticalParcellation . . . 11 matches
...[[FreeSurferWiki|top]] = Cortical Parcellation = The FreeSurfer utilities [[mris_ca_train]] and [[mris_ca_label]] together implement a technique for automatically assigning a neur...

6.6k - rev: 44 (current) last modified: 2021-04-29 10:56:24

BuildYourOwnMonteCarlo . . . 10 matches
...FreeSurfer offers several ways to correct for multiple comparisons on the surface. One way is similar to Gaussian Random Fields (GRF) but uses a simulation rather than analitic equ...

3.8k - rev: 9 (current) last modified: 2016-04-14 17:48:33

SurfaceRegAndTemplates . . . 9 matches
...s>> = Overview = This page provides an overview of two related topics: * How the !FreeSurfer pipeline registers the surfaces of individual subjects to an "average" reference sur...

8.2k - rev: 39 (current) last modified: 2011-05-16 10:21:28

LongitudinalProcessing45 . . . 9 matches
...itudinal Stream (FS 4.5 and 5.0) = '''WARNING:''' <<BR>> The longitudinal stream in FreeSurfer 5.0 (distribution package) is broken!<<BR>> PLEASE LOAD FIXED BINARIES (links here: ...

14.8k - rev: 7 (current) last modified: 2011-04-18 13:09:05

FsTutorial/MulitModalFmriIndividual . . . 9 matches
...orial is to get you acquainted with the concepts need to perform fMRI integration in FreeSurfer by interacting with the data from an individual subject. You will not learn how to p...

8.2k - rev: 4 (current) last modified: 2009-01-13 16:56:50

FsTutorial/GroupAnalysis_tktools . . . 9 matches
... are the commands that you need to run before getting started: {{{ tcsh source your_freesurfer_dir/SetUpFreeSurfer.csh setenv SUBJECTS_DIR $TUTORIAL_DATA/buckner_data/tutorial_sub...

14.9k - rev: 132 (current) last modified: 2014-01-28 16:08:46

FsPalm . . . 9 matches
...{{{#!html <h1>Integrating FreeSurfer and PALM</h1> }}} <<TableOfContents(3)>> === Introduction === fspalm is a FreeSurfer script written to aid in the use of Permutation Analysis ...

8.0k - rev: 18 (current) last modified: 2022-03-27 17:21:25

CoursePrep . . . 9 matches
...= How to Prepare for the FreeSurfer Course = == "Required" Preparation == If you are a beginner to !FreeSurfer, the following content is HIGHLY recommended to enhance your enjoym...

2.7k - rev: 24 (current) last modified: 2019-08-29 10:42:30

Brainstorm . . . 9 matches
...analysis (visualization, processing and advanced source modeling). Integration with Freesurfer (product of François Tade) includes the following: == Subject co-registration == Th...

2.0k - rev: 7 (current) last modified: 2013-08-13 10:17:13

mri_vol2vol . . . 8 matches
...vol - Resamples a volume into another field-of-view using varous types of matrices (!FreeSurfer, FSL, SPM, and MNI). = Synopsis = mri_vol2vol = Arguments = == Required Flagged ...

8.5k - rev: 11 (current) last modified: 2017-10-04 08:29:34

UnixTutorial . . . 8 matches
...nals? == Throughout this course you will be using the Unix terminal to interact with FreeSurfer and access data. Many computer programs for scientific use are designed to be operat...

10.5k - rev: 35 (current) last modified: 2019-09-23 07:42:40

SynthSR . . . 8 matches
...= SynthSR = '''''This functionality was made available in version 7.3.0 of FreeSurfer.''''' <<BR>> <<BR>> '''''Please note that version 2.0 of the tool was released in the develop...

7.9k - rev: 28 (current) last modified: 2023-02-08 10:39:01

SubmillimeterRecon . . . 8 matches
...bmillimeter resolution = See also HighFieldRecon This page describes how to run the FreeSurfer recon-all for data with voxel sizes less than 1mm3 at native resolution. Several Fre...

4.4k - rev: 14 (current) last modified: 2017-10-28 16:07:43

SoftwareEngineer . . . 8 matches
... = Software Engineer - Job Opening = FreeSurfer is a multi-platform suite of software tools for the analysis of brain imaging data in use by thousands of neuroscientists, enginee...

4.5k - rev: 55 (current) last modified: 2017-07-24 12:52:02

PetSurferKmTutorial . . . 8 matches
...effect in the bindind potentials. = Getting the Data (not necessary for the Boston FreeSurfer Course) = = Analyzing an Individual Subject = Change directory into the project fol...

9.6k - rev: 16 (current) last modified: 2019-09-25 18:21:27

LabelsClutsAnnotationFiles . . . 8 matches
...Color Lookup Tables and Annotation Files = This page discusses the basic concepts of FreeSurfer files that relate to identifying regions-of-interest for surfaces and volumes, namel...

12.5k - rev: 43 (current) last modified: 2018-09-28 13:42:03

FsTutorial/FuncRegistration . . . 8 matches
...[[FsTutorial|top]] | [[FsTutorial/SpmFreeSurfer|previous]] == FreeSurfer Tutorial: Registration of functional and structural data (25 minutes of exercises) == In FreeSurfer, a pa...

3.7k - rev: 10 (current) last modified: 2008-04-29 11:45:55

FsFastTutorialV4.5/930_Run_functional_and_structural_registration . . . 8 matches
...ctory where you keep the subjects whose anatomical data have been reconstructed with FreeSurfer.. === INTERFACING WITH FREESURFER === Linking into Freesurfer allows the user to v...

8.7k - rev: 5 (current) last modified: 2011-05-19 15:29:07

infantFS . . . 7 matches
...__ '''Code''': (June 2025) The infant_fs code is now merged with the main branch of FreeSurfer. You can download the dev version from [[https://surfer.nmr.mgh.harvard.edu/pub/dist...

8.9k - rev: 36 (current) last modified: 2025-06-17 10:46:33

bbregister . . . 7 matches
... required that you have an anatomical scan of the subject that has been analyzed in freesurfer. Those using bbregister should site: Greve, D. N., and Fischl, B. (2009). "Accurate...

7.7k - rev: 7 (current) last modified: 2019-07-11 13:35:54

ResearchAssistant . . . 7 matches
... working in a fast-paced computational neuroimaging lab well known for its software, FreeSurfer. The lab is comprised of faculty, postdocs, graduate students, and research assistan...

10.0k - rev: 35 (current) last modified: 2022-10-26 10:24:45

QATools . . . 7 matches
...= FreeSurfer 5.3 QA Tools = == Deprecated == Note: The QA tools described in this page were developed for !FreeSurfer 5.3. For versions 7+, use the following executable to comput...

5.9k - rev: 109 (current) last modified: 2021-08-12 10:51:08

NextGenCode . . . 7 matches
... <<TableOfContents(3)>> ''a grab-bag of notes on what we'd like to see in the ideal freesurfer source code environment, and runtime'' == Newer respository == * evaluate DVCS li...

3.7k - rev: 23 (current) last modified: 2021-05-10 08:27:20

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