FSL Group
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
where "5" is contrast of interest.