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methodology meetings

. . . They gave us tools, powerful tools.... . . . ... but if the only tool you have is a hammer

Antony
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methodology meetings

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    1. Methodology Meetings

    3. ... but if the only tool you have is a hammer then everything looks like a nail.

    7. Brain Voyager SPM-like (analysis of fMRI data, visualization) + deterministic DTI Windows, Linux, Macintosh Pros: unsurpassed interactivity, interfaces with Matlab, users can add plugins (ICA, Granger Causality, ....)? Cons: proprietary, closed, costs money (~ 5k euro), bad documentation (but wiki), no probabilistic DTI

    8. AFNI SPM-like (analysis of fMRI data, visualization)? Unix/Linux Pros: free, open source, extreme flexibility Cons: basically, command line only

    9. MedINRIA MRIcro/N-like (visualization, combination) + registration + DTI tracking, combination, visualizazion etc. Windows, Linux, Macintosh Pros: free, open source, excellent for deterministic DTI Cons: no probabilistic DTI

    10. Caret MRIcro/N-like (visualization, combination); 'viewing, manipulating, and analyzing surface reconstructions of the cerebral and cerebellar cortex' Windows, Linux, Macintosh Pros: free, open source, excellent for combining anatomical/funcional data. Includes PALS. Outstanding doc. Cons: huge amount of options, menus, etc. Van Essen, DC. A Population-Average, Landmark- and Surface-based (PALS) atlas of human cerebral cortex. Neuroimage, September 2005.

    11. R - AnalyzeFMRI R ~ Matlab -> unlimited flexibility in number manipulation AnalyzeFMRI -> extract/write data from/to Analyze/NIFTI Windows, Linux, Macintosh

    12. R - AnalyzeFMRI surgeon <- function(what2write, pathandname)? { #print("sono dentro surgeon")? sizeofHdrlastpart <- 89 sizeofHdrfirstpart <- 254 Xorig <- -20 Yorig <- -8 Zorig <- -7 #data saved, but the origin defaults to 8224, 8224, 8224 f.write.analyze(what2write, pathandname, "float", c(3,3,3))? #print("scritta mappa")? #open the same file for surgery zz<-file(paste(pathandname,".hdr",sep=""),open="rb")? #the file beginning is read and saved for the future foobeginning <- readBin(zz, what="raw", n=sizeofHdrfirstpart, size=1)?

    13. R - AnalyzeFMRI surgeon <- function(what2write, pathandname)? { #print("sono dentro surgeon")? sizeofHdrlastpart <- 89 sizeofHdrfirstpart <- 254 Xorig <- -20 Yorig <- -8 Zorig <- -7 #data saved, but the origin defaults to 8224, 8224, 8224 f.write.analyze(what2write, pathandname, "float", c(3,3,3))? #print("scritta mappa")? #open the same file for surgery zz<-file(paste(pathandname,".hdr",sep=""),open="rb")? #the file beginning is read and saved for the future foobeginning <- readBin(zz, what="raw", n=sizeofHdrfirstpart, size=1)?

    14. R - AnalyzeFMRI #write origin coordinates writeBin(as.integer(Xorig),zz,size=2)? writeBin(as.integer(Yorig),zz,size=2)? writeBin(as.integer(Zorig),zz,size=2)? #write file end writeBin(fooend,zz)? #that's it. close(zz)? }

    15. R - AnalyzeFMRI Random Fields N2G models Smoothing Statistical Thresholding (Bonferroni, FDR, RF)? FastICA read/write Analyze/NIFTI

    16. FSL

    17. FSL

    18. FSL

    19. FSL

    20. FSL

    21. FSL

    22. FSL

    23. FSL

    24. FSL

    25. FSL - fslmaths

    26. FSL - fslmaths

    27. FSL - fslmaths

    28. FSL - /usr/loca/fsl/bin

    29. FSL - scripting

    30. FSL - scripting

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