FreeSurfer protocols

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FreeSurfer specifications

Information


Unique identifier OMICS_15270
Name FreeSurfer
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use License purchase required
Operating system Unix/Linux, Mac OS
Computer skills Medium
Version 6.0
Stability Stable
Requirements
MATLAB
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/FreeSurfer

Subtool


  • BBR

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Versioning


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Maintainer


  • person_outline Bruce Fischl <>

Additional information


http://surfer.nmr.mgh.harvard.edu/fswiki

Publications for FreeSurfer

library_books

FreeSurfer.

2012 Neuroimage
PMCID: 3685476
PMID: 22248573
DOI: 10.1016/j.neuroimage.2012.01.021

FreeSurfer in pipelines

 (10)
2017
PMCID: 5664981
PMID: 29152222
DOI: 10.5256/f1000research.12934.r24599

[…] by fmriprep that illustrate all mayor preprocessing steps (t1 skullstripping, t1 to mni coregistration, epi skullstripping, epi to t1 coregistration, and compcor regions of interest)., all the freesurfer derivatives are organized under freesurfer/sub-<participant_label>/ according to the freesurfer native file organization scheme., the results of the single subject task modeling […]

2017
PMCID: 5664981
PMID: 29152222
DOI: 10.5256/f1000research.12934.r24599

[…] even more important considering that results did change with after minor version changes.page 2, 1st column, 4th paragraph of the methods: as written, a reader may think that the input images to freesurfer were those non-linearly aligned to the mni space, which surely was not the case. but if that was, then the fs analysis would have to re-done as the warps affect thickness and area […]

2017
PMCID: 5664981
PMID: 29152222
DOI: 10.5256/f1000research.12934.r24599

[…] even more important considering that results did change with after minor version changes., page 2, 1st column, 4th paragraph of the methods: as written, a reader may think that the input images to freesurfer were those non-linearly aligned to the mni space, which surely was not the case. but if that was, then the fs analysis would have to re-done as the warps affect thickness and area […]

2017
PMCID: 5837328
PMID: 28364550
DOI: 10.1093/brain/awx004

[…] the same mri protocol., to import structural and diffusion mri data in the virtual brain, the data were processed using scripts (). this processing pipeline makes use of various tools such as freesurfer (), fsl (), mrtrix3 (tournier) and remesher () to reconstruct the individual cortical surface and large-scale connectivity. the surface was reconstructed using 20 000 vertices. cortical […]

2016
PMCID: 4983151
PMID: 27547729
DOI: 10.1016/j.nicl.2016.07.010

[…] appropriate using the dt_rotate_bvecs tool. all diffusion data was reconstructed using generalised q-sampling imaging () with a diffusion sampling length ratio of 1.25. the diffusion data and the freesurfer processed t1 image were then linearly registered to the same space, and the freesurfer segmented corpus callosum () used as a seed region for tracking. grey matter regions were combined […]


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FreeSurfer in publications

 (229)
PMCID: 5953013
PMID: 29739127
DOI: 10.9758/cpn.2018.16.2.144

[…] where the wm tracts were labeled manually. this prior information is the probability of each tract to travel through or next to each of the cortical and subcortical segmentation labels from freesurfer. based on this data, tracula can reconstruct 18 major wm tracts from local diffusion orientation of each subject’s ball and stick model. the 18 available wms are corticospinal tract (cst), […]

PMCID: 5883331
PMID: 29274746
DOI: 10.1016/j.neuroimage.2017.12.060

[…] readout bandwidth bw = 425 hz/pixel. a pilot study demonstrated satisfactory levels of between-site reliability in mpm data acquisition ()., we used a standard automated processing pipeline (freesurfer v5.3) for skull stripping, tissue classification, surface extraction and cortical parcellation (http://surfer.nmr.mgn.harvard.edu) applied to longitudinal relaxation rate (r1) maps. […]

PMCID: 5945606
PMID: 29597156
DOI: 10.1016/j.dcn.2018.03.009

[…] repeated until only acceptable scans were included in the longitudinal processing (note that single time points were also processed longitudinally). no manual editing was performed., finally, using freesurfer 6.0, the t1-weighthed images were processed using a novel automated algorithm for longitudinal segmentation of hippocampal subregions (, ) (). the procedure uses a computational atlas […]

PMCID: 5896261
DOI: 10.1155/2018/8039075

[…] []. motion correction was not performed; however, based on visual assessment, examinations with substantial motion artifacts were carefully excluded. t1 volumetric examinations were analyzed with freesurfer [], which provides regions-of-interest across a participant's brain along with a variety of localized measurements therein. the extracted measurements are all structural and based […]

PMCID: 5868123
PMID: 29615893
DOI: 10.3389/fnagi.2018.00071

[…] task runs in total with pictures in different facial expressions of positive, neutral and negative., the brain parcellation and segmentation were conducted using the standard recon-all script of freesurfer package (fischl, ) with default settings for all procedures. volumes of 97 subcortical regions and 68 cortical areas from freesurfer recommended template were included as region […]


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FreeSurfer institution(s)
Athinoula A Martinos Center, Department of Radiology, MGH, Harvard Medical School, MA, USA
FreeSurfer funding source(s)
Supported partly by the National Center for Research Resources (P41-RR14075, and the NCRR BIRN Morphometric Project BIRN002, U24-RR021382), the National Institute for Biomedical Imaging and Bioengineering (R01EB006758), the National Institute on Aging (AG022381), the National Center for Alternative Medicine (RC1-AT005728-01), the National Institute for Neurological Disorders and Stroke (R01-NS052585-01, 1R21NS072652-01, 1R01NS070963), by Shared Instrumentation Grants 1S10RR023401, 1S10RR019307, and 1S10RR023043, and by The Autism & Dyslexia Project funded by the Ellison Medical Foundation.

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