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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 [2023/02/23 18:43] (current)
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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: 2023/02/23 18:43 (external edit)

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