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* 1. Brain Mask * 1. Brain Mask [[BR]]
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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. 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. The first stage (above) just computes the in-brain mean; the second stage is actually perfromed during the analysis.

The FS-FAST program "preproc-sess" will perform all of these stages. You can run it something like:
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["preproc-sess"] -smout fmcsm5 -fwhm 5 -s sessid
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There are a lot of things going on "under the hood", so I'll explain each one.-s sessid tells preproc-sess the name of the session as created with unpacksdcmdir. Once it has the session, it can find the raw data in sessid/bold/RRR as f.bhdr (RRR is a run number). It will use the first time point of the first run as a template for both motion correction and brain masking. The brain mask is created using FSL's bet program. The result is stored in bold/masks/brain.bhdr. This is a "binary" mask, ie, each voxel is either 0 (not in the brain) or 1 (in the brain).
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["preproc-sess"] -smout <smfmc6> -fwhm <fwhm>

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 BR * 2. Motion Correction * 3. Slice-Timing Correction * 4. Spatial Smoothing * 5. Intensity Normalization (inorm)

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. The first stage (above) just computes the in-brain mean; the second stage is actually perfromed during the analysis.

The FS-FAST program "preproc-sess" will perform all of these stages. You can run it something like:

["preproc-sess"] -smout fmcsm5 -fwhm 5 -s sessid

There are a lot of things going on "under the hood", so I'll explain each one.-s sessid tells preproc-sess the name of the session as created with unpacksdcmdir. Once it has the session, it can find the raw data in sessid/bold/RRR as f.bhdr (RRR is a run number). It will use the first time point of the first run as a template for both motion correction and brain masking. The brain mask is created using FSL's bet program. The result is stored in bold/masks/brain.bhdr. This is a "binary" mask, ie, each voxel is either 0 (not in the brain) or 1 (in the brain).

  • <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"].

FsFastPreprocessData (last edited 2009-02-13 10:18:36 by DanielGoldenholz)