civet.getFilename | R Documentation |
Returns either one or more Civet filenames, depending on file type.
civet.getFilenameClassify( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameGrayMatterPve( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameWhiteMatterPve( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameCsfPve( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameStxT1( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameCerebrumMask( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameSkullMask( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameGrayMatterSurfaces( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameWhiteMatterSurfaces( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameMidSurfaces( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenamesCorticalThickness( scanID, baseDir, civetVersion = "1.1.9", smoothing = "20mm", fullPath = TRUE ) civet.getFilenamesCorticalArea( scanID, baseDir, civetVersion = "1.1.9", smoothing = "40mm", fullPath = TRUE ) civet.getFilenamesCorticalVolume( scanID, baseDir, civetVersion = "1.1.9", smoothing = "40mm", fullPath = TRUE ) civet.getFilenameMeanSurfaceCurvature( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameLinearTransform( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE ) civet.getFilenameNonlinearTransform( scanID, baseDir, civetVersion = "1.1.9", fullPath = TRUE )
scanID |
A string specifying the unique scan-id (and thus sub-directory) within the Civet root output directory. |
baseDir |
A string specifying the Civet root output directory. This directory will, in turn, contain all of the scanIDs. |
civetVersion |
An optional string specifying the version of Civet used to create the output. This is significant since filenames and directory structures may change across difference versions of Civet. |
fullPath |
A boolean specifying whether the function is to return either a fully-qualified path (TRUE) or just the filename without path (FALSE). |
smoothing |
A character code indicating the smoothing level used in computing thickness, area, or volume e.g. "20mm" |
The purpose of this function is to facilitate writing code requiring manipulation of Civet products. To this purpose, we have written a number of convenience functions which, given the type of file desired and a path to the Civet output directory, are able to determine and return the actual filename(s).
Either a string or a list is returned, depending on the number of filenames returned. Specifically, a single filename is returned as a string, whereas multiple filenames are returned as named lists.
civet.getFilenameClassify
: Tissue classification
civet.getFilenameGrayMatterPve
: gray matter pve
civet.getFilenameWhiteMatterPve
: white matter pve
civet.getFilenameCsfPve
: csf pve
civet.getFilenameStxT1
: Standard to T1 transform
civet.getFilenameCerebrumMask
: brain mask
civet.getFilenameSkullMask
: skull mask
civet.getFilenameGrayMatterSurfaces
: gray matter surfaces
civet.getFilenameWhiteMatterSurfaces
: white matter surfaces
civet.getFilenameMidSurfaces
: mid surfaces
civet.getFilenamesCorticalThickness
: cortical thickness
civet.getFilenamesCorticalArea
: cortical area
civet.getFilenamesCorticalVolume
: cortical volume
civet.getFilenameMeanSurfaceCurvature
: surface curvature
civet.getFilenameLinearTransform
: linear transform
civet.getFilenameNonlinearTransform
: non-linear transform
Jim Nikelski nikelski@bic.mni.mcgill.ca
## Not run: library(RMINC) # set Civet root path and scan-identifier basePath <- "~/tmp/ADNI/civet/pipeOut" scanID = "0221-M-AD" # get the name of the aggregate tissue classification volume # ... and then read it classifyVolname <- civet.getFilenameClassify(scanID, basePath) classifyVol <- mincIO.readVolume(classifyVolname) # get the left and right gray matter surface filenames and then # ... print the names gmSurfName <- civet.getFilenameGrayMatterSurfaces(scanID, basePath) print(gmSurfName$left) print(gmSurfName$right) # get the various transformation file filenames lin.xfmName <- civet.getFilenameLinearTransform(scanID, basePath) print(lin.xfmName) nlin.xfmNames <- civet.getFilenameNonlinearTransform(scanID, basePath) print(nlin.xfmNames$xfm) # name of the nlin xfm file print(nlin.xfmNames$grid) # name of the nlin grid file ## End(Not run)
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