biac:analysis:resting_pipeline
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biac:analysis:resting_pipeline [2013/09/16 18:26] – admin | biac:analysis:resting_pipeline [2013/09/17 13:59] – [Step 6] admin | ||
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0.5 | 0.5 | ||
--lpfreq=0.08 | --lpfreq=0.08 | ||
- | is .08hz | + | is .08hz. highpass is fixed at .001hz. |
--corrlabel=FILE | --corrlabel=FILE | ||
correlation search. default is the 116 region AAL | correlation search. default is the 116 region AAL | ||
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==== Step 6 ==== | ==== Step 6 ==== | ||
* this step will band-pass filter data to remove high-frequency noise using custom python code | * this step will band-pass filter data to remove high-frequency noise using custom python code | ||
- | * the default is 0.08 HZ | + | * the default |
+ | * highpass is fixed at .001 HZ | ||
* if you'd like to chose a different frequency, please use ** --lpfreq ** | * if you'd like to chose a different frequency, please use ** --lpfreq ** | ||
==== Step 7 ==== | ==== Step 7 ==== | ||
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</ | </ | ||
+ | |||
+ | ==== Step 8 ==== | ||
+ | * Functional connectivity density mapping | ||
+ | * Takes functional data from last step and calculates how connected they are to the voxels around them | ||
+ | * uses ( --fcdmthresh and --refgm ) as the pearson r-value and gray matter mask | ||
+ | * if defaults are used, then a dilated gray matter mask is used from FAST segmentation of MNI brain and a pearson r value of 0.6 | ||
+ | * Iteratively goes to all neighboring voxels and counts the number that have correlated signal until they are under the r threshold | ||
+ | * adapted from Dardo Tomasi, PNAS(2010), vol. 107, no. 21. 9885–9890 | ||
+ | * resulting file with be " | ||
+ | |||
+ | {{: | ||
===== Things to consider ===== | ===== Things to consider ===== | ||
* this was designed to be modular, so that you only need to run the steps you need | * this was designed to be modular, so that you only need to run the steps you need |
biac/analysis/resting_pipeline.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1