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biac:analysis:physiological [2011/11/22 14:26] gadde |
biac:analysis:physiological [2022/01/18 16:09] cmp12 |
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====== Physiological Correction Methods ====== | ====== Physiological Correction Methods ====== | ||
+ | |||
+ | ===== Generate resampled TSV from raw GE physio files automatically copied from the scanners | ||
+ | |||
+ | < | ||
+ | [cmp12@blade17 20211218_03399]$ / | ||
+ | usage: convert_GEphysio.py [-h] --xmlh XMLFNAME [--json JSONFNAME] --physdir | ||
+ | | ||
+ | | ||
+ | |||
+ | create 100Hz resampled TSV from raw GE physio data | ||
+ | |||
+ | optional arguments: | ||
+ | -h, --help | ||
+ | --xmlh XMLFNAME | ||
+ | --json JSONFNAME | ||
+ | --physdir PHYSDIR | ||
+ | --bidsout | ||
+ | --afnislicetime | ||
+ | --delay DELAYTIME | ||
+ | | ||
+ | |||
+ | </ | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ===== CIGAL specific ===== | ||
Currently this assumes that you have recorded your physiological responses through Cigal. | Currently this assumes that you have recorded your physiological responses through Cigal. | ||
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Opt.Nslices = 34 | Opt.Nslices = 34 | ||
Opt.PhysFS = 100 | Opt.PhysFS = 100 | ||
+ | Opt.SliceOrder = ' | ||
+ | %please choose the correct order if not running interleaved: | ||
RetroTS(Opt) | RetroTS(Opt) | ||
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- | ===== FSL Feat ===== | ||
- | |||
- | We've gotten the FSL beta functions for physiological correction, which we'll test. | ||
- | |||
- | They are based on the same algorithms used in afni with retroicor. | ||
- | |||
- | More information can be seen here: | ||
- | [[http:// | ||
- | |||
- | The beta options will allow you to plug in the resulting regressors directly into Feat. After pre-processing you can use the **res4d.nii.gz** files for further analysis ( filtered_func_data would not have the physio regressor removed ). | ||