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biac:analysis:resting_pipeline

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biac:analysis:resting_pipeline [2016/11/08 15:28]
cmp12 [Download Source]
biac:analysis:resting_pipeline [2019/05/31 13:27] (current)
cmp12
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                         (1,​3,​5,​2,​4,​6),​ up=ascending,​ down=descending,​                         (1,​3,​5,​2,​4,​6),​ up=ascending,​ down=descending,​
                         even=interleaved (2,​4,​6,​1,​3,​5) ).  Default is to read                         even=interleaved (2,​4,​6,​1,​3,​5) ).  Default is to read
-                        this from input image, if available.+                        this from input BXH, if available.
   --tr=MSEC ​            TR of functional data in MSEC   --tr=MSEC ​            TR of functional data in MSEC
   --ref=FILE ​           pointer to FLIRT reference image if not using standard   --ref=FILE ​           pointer to FLIRT reference image if not using standard
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   * run fsl's slice time correction ( slicetimer )   * run fsl's slice time correction ( slicetimer )
   * if starting with a BXH header, you'll likely have the sliceorder field which will be used to create a custom sliceorder file to be used by fsl   * if starting with a BXH header, you'll likely have the sliceorder field which will be used to create a custom sliceorder file to be used by fsl
 +  * the default is to run bxh_slicetiming to extract a timing file from the BXH header
   * if this isn't present, then you'll need to define **--sliceorder** so that we can generate the file for you   * if this isn't present, then you'll need to define **--sliceorder** so that we can generate the file for you
     * "​odd"​ is interleaved with odd, then even slice ordering: 1,​3,​5,​2,​4,​6,​etc     * "​odd"​ is interleaved with odd, then even slice ordering: 1,​3,​5,​2,​4,​6,​etc
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     * "​up"​ is ascending data, from the bottom up: 1,2,3,4,5,6     * "​up"​ is ascending data, from the bottom up: 1,2,3,4,5,6
     * "​down"​ is descending data, from the top down: 6,5,4,3,2,1     * "​down"​ is descending data, from the top down: 6,5,4,3,2,1
 +  * this gets much more complicated with multi-band data, so using the default extraction is recommended ​
  
 ==== Step 2 ==== ==== Step 2 ====
biac/analysis/resting_pipeline.txt · Last modified: 2019/05/31 13:27 by cmp12