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| ["preproc-sess"] -smout [smfmc6] -fwhm [6] | Preprocessing specifically refers to anything that is done to the data prior to computing a standard deviation, but can also include various other things (eg, computing masks). In FS-FAST, these are the preprocessing steps: |
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| [[BR]] | * 1. Brain Mask * 2. Motion Correction * 3. Slice-Timing Correction * 4. Spatial Smoothing * 5. Intensity Normalization (inorm) |
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| This procedure consists of several sub-steps that can be invoked individually. They should only be run instead of, not in addition to ["preproc-sess"]. 1. [[Include(FsFastMotionCorrect, , 6)]] |
The FS-FAST program "preproc-sess" will perform all of these stages. It is not necessary to perform all these stages. Note that B0 correction is not yet avaialble in FS-FAST. Most of these stages are self-explanatory. Brain Mask does a quick segmentation of the brain from the rest of the volume. Intensity normalization is the processes of rescaling all intensity values within a 4D data set so that the in-brain mean is 1000. Intensity normalization is actually done in two stages. |
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| 1. [[Include(FsFastSmooth, , 6)]] | |
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| 1. [[Include(FsFastNormalizeIntensity, , 6)]] | |
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| 1. [[Include(FsFastMakeBrainMask, , 6)]] | ["preproc-sess"] -smout <smfmc6> -fwhm <fwhm> <fwhm>=6 is typical. Check <smfmc6>.report in functional subdirectory for indications of problems with data. See ["FsFastTutorial/800 Normalize signal intensity"] for details. Check severity of motion by plotting motion correction translation component versus time point with ["plot-twf-sess"]. |
Preprocessing specifically refers to anything that is done to the data prior to computing a standard deviation, but can also include various other things (eg, computing masks). In FS-FAST, these are the preprocessing steps:
* 1. Brain Mask * 2. Motion Correction * 3. Slice-Timing Correction * 4. Spatial Smoothing * 5. Intensity Normalization (inorm)
The FS-FAST program "preproc-sess" will perform all of these stages. It is not necessary to perform all these stages. Note that B0 correction is not yet avaialble in FS-FAST. Most of these stages are self-explanatory. Brain Mask does a quick segmentation of the brain from the rest of the volume. Intensity normalization is the processes of rescaling all intensity values within a 4D data set so that the in-brain mean is 1000. Intensity normalization is actually done in two stages.
["preproc-sess"] -smout <smfmc6> -fwhm <fwhm>
<fwhm>=6 is typical.
Check <smfmc6>.report in functional subdirectory for indications of problems with data. See ["FsFastTutorial/800 Normalize signal intensity"] for details. Check severity of motion by plotting motion correction translation component versus time point with ["plot-twf-sess"].