User Tools

Site Tools


biac:analysis:resting_pipeline

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
biac:analysis:resting_pipeline [2014/08/04 16:03]
127.0.0.1 external edit
biac:analysis:resting_pipeline [2019/05/31 13:27]
cmp12
Line 47: Line 47:
                         (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
Line 181: Line 181:
   * 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
Line 186: Line 187:
     * "​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 ====
Line 430: Line 432:
   - need a working install of the [[http://​www.nitrc.org/​projects/​bxh_xcede_tools/​|BIRN BXH/Xcede tools]]   - need a working install of the [[http://​www.nitrc.org/​projects/​bxh_xcede_tools/​|BIRN BXH/Xcede tools]]
   - will need to edit any paths that may be different at your install location ( FSL FAST segmentations of the MNI brain and base sets of ROIs )   - will need to edit any paths that may be different at your install location ( FSL FAST segmentations of the MNI brain and base sets of ROIs )
-  - **Chen et al. holder**+  - **Chou et al. AJNAR(2012),​ May; 33(5): 833–838 ​**
   - fcdm algorithm adapted from **Dardo Tomasi, PNAS(2010), vol. 107, no. 21. 9885–9890**   - fcdm algorithm adapted from **Dardo Tomasi, PNAS(2010), vol. 107, no. 21. 9885–9890**
  
biac/analysis/resting_pipeline.txt · Last modified: 2019/05/31 13:27 by cmp12