biac:analysis:resting_pipeline
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| Both sides previous revisionPrevious revision | Next revisionBoth sides next revision | ||
| biac:analysis:resting_pipeline [2012/07/09 18:57] – [Python/FSL Resting State Pipeline] admin | biac:analysis:resting_pipeline [2012/07/09 18:59] – [Step 3] admin | ||
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| * the functional run is meaned across time with fslmaths, then bet is applied. | * the functional run is meaned across time with fslmaths, then bet is applied. | ||
| * if you find that bet is doing a poor job finding the edges you can adjust the intensity threshold with **--betfval** | * if you find that bet is doing a poor job finding the edges you can adjust the intensity threshold with **--betfval** | ||
| - | * this is equivalent of **-f** when actually running bet. the default is 0.5, but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask ) | + | * this is equivalent of **-f** when actually running bet. the default is 0.4 (same as feat), but smaller values will be more conservative in finding the edges of the brain ( ie: larger mask ) |
| + | * if provided T1 anatomical is skull stripped. **--anatbetfval** is used to control intensity threshold, the default is 0.5 (same as feat) | ||
| ==== Step 4 ==== | ==== Step 4 ==== | ||
| * normalize the data using flirt | * normalize the data using flirt | ||
biac/analysis/resting_pipeline.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1