biac:analysis:resting_pipeline
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revision | ||
biac:analysis:resting_pipeline [2014/02/10 20:16] – [Download Source] cmp12 | biac:analysis:resting_pipeline [2024/06/21 15:44] (current) – external edit 127.0.0.1 | ||
---|---|---|---|
Line 47: | Line 47: | ||
(1, | (1, | ||
even=interleaved (2, | even=interleaved (2, | ||
- | this from input image, if available. | + | this from input BXH, if available. |
--tr=MSEC | --tr=MSEC | ||
--ref=FILE | --ref=FILE | ||
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 | ||
* " | * " | ||
Line 186: | Line 187: | ||
* " | * " | ||
* " | * " | ||
+ | * this gets much more complicated with multi-band data, so using the default extraction is recommended | ||
==== Step 2 ==== | ==== Step 2 ==== | ||
Line 429: | Line 431: | ||
- source files assume you have a working install of FSL and all imported python modules | - source files assume you have a working install of FSL and all imported python modules | ||
- need a working install of the [[http:// | - need a working install of the [[http:// | ||
- | - **Chen et al. holder** | + | |
+ | | ||
- 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: 2024/06/21 15:44 by 127.0.0.1