spm5_preprojobs
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— | spm5_preprojobs [2011/04/03 04:23] (current) – created jochen | ||
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+ | ====== spm5_preprojobs ====== | ||
+ | |||
+ | ===== Motivation ===== | ||
+ | As said on the page describing the [[Processing stream - preprocessing|UI-based configuration of SPM5/SPM8 preprocessing]] in NeuroElf, this function is mostly meant to ensure that all subjects are preprocessed using the same parameters (and that all steps are performed in their entirety and same order). | ||
+ | |||
+ | ===== Requirements ===== | ||
+ | See the [[Processing stream - preprocessing|page on the GUI]]. | ||
+ | |||
+ | ===== Function reference ('help spm5_preprojobs' | ||
+ | < | ||
+ | |||
+ | FORMAT: | ||
+ | FORMAT: | ||
+ | |||
+ | Input fields: | ||
+ | |||
+ | sf subject (base) folder | ||
+ | fp functional folder pattern (e.g. f*/r*) | ||
+ | ap anatomical folder pattern (e.g. a*/*) | ||
+ | opts 1x1 struct with options | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
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+ | | ||
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+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | ' | ||
+ | | ||
+ | | ||
+ | | ||
+ | | ||
+ | (default: [-78, -114, -54; 78, 78, 84]) | ||
+ | | ||
+ | | ||
+ | |||
+ | Output fields: | ||
+ | |||
+ | jobs cell array with jobs suitable for spm_jobman | ||
+ | jobhelps | ||
+ | ff cell array with functional files (after preprocessing) | ||
+ | |||
+ | Note: without inputs, the UI-based mode will be used.</ | ||
+ | |||
+ | ===== Arguments and options ===== | ||
+ | |||
+ | ==== sf ==== | ||
+ | This must be a single folder name (the UI loops over all folders matching a pattern!) containing separate folders for the anatomical and each functional scan (run). | ||
+ | |||
+ | ==== fp ==== | ||
+ | A foldername pattern, relative to the '' | ||
+ | |||
+ | ==== ap ==== | ||
+ | A foldername (or pattern), relative to the '' | ||
+ | |||
+ | ==== opts ==== | ||
+ | Optional settings in a 1x1 '' | ||
+ | |||
+ | ==== .afp ==== | ||
+ | Filename pattern for the anatomical scan (image), defaults to '' | ||
+ | |||
+ | ==== .ffp ==== | ||
+ | Filename pattern for the functional files, defaults to '' | ||
+ | |||
+ | ==== .fsingle ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .fun2str ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .jobfile ==== | ||
+ | If given and set to a valid ''' | ||
+ | |||
+ | ==== .jobrun ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .normsess ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .normtype ==== | ||
+ | Choice of normalization algorithm. One of | ||
+ | |||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | |||
+ | **Please note that the final location of activation peaks (across subjects) will differ based on your choice of normalization algorithm!** | ||
+ | |||
+ | ==== .reganat ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .reslice ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .rinterpe ==== | ||
+ | Sets the interpolation degree of SPM's sampling function for the estimation component of the realignment step. | ||
+ | |||
+ | ==== .rinterpr ==== | ||
+ | Sets the interpolation degree of SPM's sampling function for the reslicing component of the realignment step (only in effect if '' | ||
+ | |||
+ | ==== .rqual ==== | ||
+ | Sets the realignment quality value, which is a trade-off value between quality (1) and speed (smaller than 1), setting the ratio of voxels to be maximally included in the estimation of motion (see SPM's manual for further instructions). | ||
+ | |||
+ | ==== .rrtm ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .rsep ==== | ||
+ | Sets the realignment (motion estimation) sampling grid resolution (see SPM's manual for further instructions). Generally, the higher the number, the faster (and less precise) the process becomes. | ||
+ | |||
+ | ==== .skip ==== | ||
+ | Number of volumes to skip (from raw data); this can be used to " | ||
+ | |||
+ | ==== .smk ==== | ||
+ | Smoothing kernel in mm. If set to 0, smoothing step is removed from processing stream. | ||
+ | |||
+ | ==== .st ==== | ||
+ | Boolean flag, if set to '' | ||
+ | |||
+ | ==== .sto ==== | ||
+ | Sets the order of slices for the slice-timing correction step of **'' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * ''' | ||
+ | * a numeric list of all integer numbers in the range (and including) 1 through N, each number occurring exactly once | ||
+ | |||
+ | ==== .str ==== | ||
+ | Sets the reference slice number for the slice-timing correction step. | ||
+ | |||
+ | ==== .stta ==== | ||
+ | Sets the TA (time-of-acquisition in seconds) for one volume of data for the slice-timing correction step. | ||
+ | |||
+ | ==== .sttr ==== | ||
+ | Sets the TR (repetition time in seconds) for the slice-timing correction step. | ||
+ | |||
+ | ==== .wbb ==== | ||
+ | Sets the bounding box for the call to the '' | ||
+ | |||
+ | ==== .winterp ==== | ||
+ | Sets the interpolation degree of SPM's sampling function for the '' | ||
+ | |||
+ | ==== .wvox ==== | ||
+ | Sets the voxel size for the '' | ||
+ | |||
+ | ===== Usage notes ===== | ||
+ | If called without arguments, a [[Processing stream - preprocessing|UI window]] opens, that allows to configure these values interactively. If multiple subjects are found and configured, this function (spm5_preprojobs) is called for each of those subjects in turn. | ||
spm5_preprojobs.txt · Last modified: 2011/04/03 04:23 by jochen