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==About the Group==
This group is meeting weekly for one hour; we began in 8/2009. Our goal is to begin with a tutorial of basic FSL tools and related issues and eventually progress to more advanced topics. The current default meeting location is the CHS 37-415, Tuesdays AM from 10:30 to 11:30.

==Meetings==
Week 1 (8/26): Covered FSL basics. Where to install, how to run, command line vs. GUI, file types. [[Media:FSL_Workshop_1.pdf]]

Week 2 (9/1): Covered file types conversion from DICOM to NIFTI. Discussed dcm2nii and mri_convert. Reviewed image orientation, flipping issues.
[[Media:FSL_Workshop_2.pdf]]

Week 3 (9/15): Covered BET [[Media:FSL Workshop 3 BET.pdf]] and FLIRT [[Media:FSL_Workshop_3_FLIRT.pdf]]

Week 4 (9/22): Covered FEAT, part 1. fMRI pre-processing, GLM setup for single subjects. [[Media:Fsl_workshop_FEAT_week4.pdf‎]]

Week 5 (9/29): Covered FEAT, part 2. Higher-level modeling, examples of group models, standard space analysis. [[Media:FSL_workshop_FEAT_2.pdf‎]]

Week 6 (10/6): Unix intro, BASH scripting [[Media:FSL_6_BASH.pdf‎ ]]

Week 7 (10/27): FSL utilities (view, maths, etc.) [[Media:FSLWorkshop10-27.doc]]

Week 8 (11/3): More FSL utilities (stats, slicer, etc.) [[Media:FSL_Workshop_11-03.doc]]

Week 9 (11/10): ROI analyses

Week 10 (11/17): Functional connectivity [[Media:FSL_group_functional_connectivity.pdf]] [[Media:PPI_notes_11_2009.doc]]

Week 11 (12/1): ? Possibly cover motion correction or DTI

==Useful links==
* OsiriX dicom viewer: http://www.osirix-viewer.com/
* dcm2nii website: http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html http://www.sph.sc.edu/comd/rorden/mricron/install.html
* FSL website: http://www.fmrib.ox.ac.uk/fsl/index.html
* FSL mailing list: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl
* Unix tutorial: http://www.fmrib.ox.ac.uk/fslcourse/unix_intro/
* Russ Poldrack's spatial registration slides: http://ccn.ucla.edu/wiki/images/a/a1/SpatialTransformation.pdf
* FSL FLIRT tutorial: http://www.fmrib.ox.ac.uk/fslcourse/lectures/reg.pdf
* Russ Poldrack's fMRI preprocessing slides: http://www.ccn.ucla.edu/wiki/index.php/Principles_of_Neuroimaging_B_/_functional_MRI
* NITP summer course archived lectures (very useful):
Slides of interest: http://www.brainmapping.org/Live.php
Archived lectures: http://www.livestream.com/nitp2009
* FSL fast download: http://www.ccn.ucla.edu/fsl_course
* Unix introduction: http://www.ee.surrey.ac.uk/Teaching/Unix/
* Permissions (chmod) overview: http://www.catcode.com/teachmod/

* UCLA FSL Users list: http://lists.ucla.edu/cgi-bin/mailman/listinfo/fslusers
This list was provided by Poldrack Lab members. If people in the class are interested, we can make use of this list as a local place to exchange FSL ideas.

==Scripts==
* cluster2atlas.sh [[Media:cluster2atlas.sh]]: Returns atlas region names for all local maxima within clusters for a specific FEAT contrast, reported in the files lmax_zstatx_std.txt. Run within the FEAT directory. Command line usage is:
> ./cluster2atlas.sh 5<br>
where "5" is contrast of interest.

FSL Group - Revision history

Ccn admin: 1 revision

Mscohen: Reverted edits by Dizik (Talk); changed back to last version by Jbrown