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BasicReconstruction . . . 7 matches
...[[FreeSurferWorkFlows|top]] | [[FreeSurferWorkFlows|previous]] | [[RecommendedReconstruction|next]] This workflow completes the entire reconstruction process without stopping. Se...

2.5k - rev: 29 (current) last modified: 2008-04-29 11:45:31

tksurfer . . . 6 matches
...bert lh inflated}}} = See Also = TkSurferGuide = Author/s = KevinTeich = Links = FreeSurfer, TkSurfer = Description = TkSurfer is the surface viewer for FreeSurfer. Use it to...

6.8k - rev: 16 (current) last modified: 2011-06-27 12:05:43

mri_glmfit . . . 6 matches
...r dir ||save outputs to dir || || || ||--y inputfile || || ||--fsgd FSGDF <gd2mtx> ||freesurfer descriptor file || ||--X design matrix file || || ||--C contrast1.mat <--C contrast2...

18.3k - rev: 11 (current) last modified: 2020-11-11 12:30:18

infantFS . . . 6 matches
...__'''DOWNLOAD'''__ '''Code''': Click [[https://lcn.martinos.org/infant-freesurfer-request/|here]] to request. We have an experimental docker release image as well, s...

8.8k - rev: 31 (current) last modified: 2022-12-05 12:13:59

fcseed-sess . . . 6 matches
...ectdir || == Optional Flagged Arguments == ||-seg segid <-segid segid2 ...> ||use FreeSurfer segmentation as seed || use FreeSurfer Segmentation IDs for common ROIs (found in $F...

5.8k - rev: 10 (current) last modified: 2011-01-13 17:31:04

WorkFlows . . . 6 matches
...[[FreeSurferWiki|top]] | [[FreeSurferWorkFlows|next]] = WorkFlows = The FreeSurfer tools, and brain image processing tools in general, are best understood in the context of a wor...

1.0k - rev: 10 (current) last modified: 2008-04-29 11:45:23

ThirdPartySoftware . . . 6 matches
...[http://nipy.sourceforge.net/nipype/index.html|Nipype]] - Neuroimaging in Python, w/ FreeSurfer interfaces * [[http://mindboggle.info/data.html|Mindboggle-101 data]] - Manually la...

1.6k - rev: 5 (current) last modified: 2019-07-17 17:34:18

SynthSeg . . . 6 matches
...= SynthSeg = '''''This functionality is now available in FreeSurfer (v7.3.2 onwards)''''' <<BR>> <<BR>> <<BR>> '''''Update September 2022: SynthSeg is also available as part of Ma...

11.3k - rev: 36 (current) last modified: 2023-12-12 00:36:11

RcbfProc . . . 6 matches
...) data produced by the Siemens scanner using their pulsed ASL (PASL) protocol in the FreeSurfer environment, including registration and group analysis. This is sequence is usually ...

2.1k - rev: 6 (current) last modified: 2010-01-14 16:48:00

HistoAtlasSegmentation . . . 6 matches
...ogical Atlas "NextBrain" = '''''To use this functionality before the next version of FreeSurfer comes out, please install the latest stable version of FreeSurfer (7.4.1), download ...

4.8k - rev: 16 (current) last modified: 2024-02-16 19:00:01

FslWorkFlows . . . 6 matches
...[[FreeSurferWiki|top]] | [[WorkFlows|previous]] = FreeSurfer - FSL - FEAT Work Flows = FslWorkFlows describes processing workflows for applying FreeSurfer tools to FSL fMRI analy...

0.5k - rev: 7 (current) last modified: 2008-04-29 11:46:14

FsTutorial/VolumetricGroupAnalysis . . . 6 matches
...[[FsTutorial|top]] | [[FsTutorial|previous]] | [[FsTutorial|next]] = FreeSurfer Tutorial: Volumetric Group Analysis = * If you are taking one of the formally organized courses, th...

12.6k - rev: 3 (current) last modified: 2011-03-30 16:17:50

FsTutorial/QuestionAnswersApril2013 . . . 6 matches
...== This wiki page contains the students questions and answers from the April 29 2013 Freesurfer course. == [[https://surfer.nmr.mgh.harvard.edu/cgi-bin/fsurfer/internal/questionsl...

7.9k - rev: 13 (current) last modified: 2013-11-03 11:32:23

FsFastTutorialV6.0/TutorialData . . . 6 matches
...as 1 run (except sess01 which has 4 runs) * Collected at MGH Bay 4 (3T Siemens) * !FreeSurfer anatomical analyses = Functional Paradigm = The paradigm was designed to study the ...

2.7k - rev: 14 (current) last modified: 2018-09-30 09:41:07

FsFastTutorialV5.1/TutorialData_freeview . . . 6 matches
...has 1 run (except sess01 which has 4 runs) * Collected at MGH Bay 4 (3T Siemens) * FreeSurfer anatomical analyses = Functional Paradigm = The paradigm was designed to study the e...

3.1k - rev: 3 (current) last modified: 2015-09-30 11:32:57

sbTIV . . . 5 matches
...ippocampal volume size). The gold-standard method is manual delineation of T2 scans. Freesurfer currently provides the eTIV measure, described [[eTIV| here]]. It has been shown to ...

7.4k - rev: 72 (current) last modified: 2023-01-05 11:00:54

regdat2xfm . . . 5 matches
...(children)>> '''Index''' <<TableOfContents>> = Name = regdat2xfm - produces the MNI/Freesurfer compatible xfm which can be used for freesurfer = Synopsis = regdat2xfm srcvol targ...

1.1k - rev: 4 (current) last modified: 2008-04-29 11:45:26

mri_robust_template . . . 5 matches
...subject template in the [[LongitudinalProcessing | longitudinal stream ]] (-base) in FreeSurfer. Important Note: For best performance the input images should all have the same in...

6.0k - rev: 13 (current) last modified: 2020-05-28 10:41:38

ToolsTutorial . . . 5 matches
...'''Index''' <<TableOfContents>> = FreeSurfer Tools Tutorial = The tutorial below is meant to introduce you to several tools that are used by the !FreeSurfer Development team. To ...

4.0k - rev: 9 (current) last modified: 2009-12-22 20:06:33

SubcorticalSegmentation . . . 5 matches
...[[FreeSurferWorkFlows|top]] = Subcortical Segmentation = In automatic subcortical segmentation, each voxel in the normalized brain volume is assigned one of about 40 labels, incl...

4.9k - rev: 41 (current) last modified: 2018-01-04 15:07:58

RecommendedReconstruction . . . 5 matches
... [[FreeSurferWorkFlows|top]] | [[BasicReconstruction|previous]] | [[HistoricalReconstruction|next]] Although the reconstruction process is broken down into three different stages,...

3.7k - rev: 36 (current) last modified: 2014-08-20 11:34:47

MiDeFace . . . 5 matches
... '''mideface - a FreeSurfer tool for Minimally Invasive DeFacing of MRI images''' Note: a bug was found in the 7.4.0 version of MiDeFace when creating the head mask and true face ...

12.1k - rev: 53 (current) last modified: 2023-06-20 13:46:28

FsTutorial/CourseHistory . . . 5 matches
...ocation''' ||'''type''' ||'''attendees''' || '''auditors'''|| ||81 ||2023 ||June || !FreeSurfer Virtual Course||virtual fs ||32 ||4 || ||80 ||2022 ||Sept || !FreeSurfer Virtual Cou...

6.1k - rev: 74 (current) last modified: 2024-02-29 12:02:54

FsFastTutorialV5.1/TutorialData . . . 5 matches
...has 1 run (except sess01 which has 4 runs) * Collected at MGH Bay 4 (3T Siemens) * FreeSurfer anatomical analyses = Functional Paradigm = The paradigm was designed to study the ...

3.2k - rev: 10 (current) last modified: 2016-09-01 16:37:09

FsFastTutorialV5.1/FsFastPreProc_freeview . . . 5 matches
...essing includes 1. Template Creation 1. Brain Mask Creation 1. Registration with FreeSurfer Anatomical 1. Motion Correction 1. Slice Timing Correction (if using) 1. Spatial ...

13.2k - rev: 22 (current) last modified: 2016-04-28 14:31:58

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