biac:analysis:physiological
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biac:analysis:physiological [2011/12/08 20:46] – [AFNI details] petty | biac:analysis:physiological [2022/01/20 14:45] – cmp12 | ||
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====== Physiological Correction Methods ====== | ====== Physiological Correction Methods ====== | ||
+ | |||
+ | ===== Generate resampled TSV from raw GE physio files automatically copied from the scanners | ||
+ | |||
+ | Stock GE physio is hardcoded by GE to be 25Hz for respiration and 100Hz for pulse. | ||
+ | |||
+ | |||
+ | < | ||
+ | [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 | ||
+ | | ||
+ | |||
+ | </ | ||
+ | |||
+ | Provide a valid BXH ( and JSON if possible ) and a path to your subject physio folder to convert_GEphysio.py function. | ||
+ | |||
+ | This function will search the physio directory for physio files within a specified time range based on the functional scantime + timepoints + a default delay in writing. | ||
+ | |||
+ | If matching respiration and pulse files are found theoretical scan triggers on each TR will be created and the respiration and pulse data will be resampled to 100Hz and locked to the onset of the scan. If disdaqs are detected in the BXH the corresponding physio time will be discarded. | ||
+ | |||
+ | < | ||
+ | / | ||
+ | </ | ||
+ | |||
+ | By default you will get a 100Hz resampled TSV with headers and timing. | ||
+ | |||
+ | |||
+ | The **--bidsout** flag will output a TSV without headers and a BIDS sidecar with appropriate column labels and sampling frequency. | ||
+ | |||
+ | |||
+ | The **--afnislicetime** flag will output two 1D slicetiming files to be used with RetroTS.py and afni_proc.py directly. | ||
+ | |||
+ | === Using afni === | ||
+ | |||
+ | You can create regressors for afni preprocessing from output files above using RetroTS.py | ||
+ | |||
+ | < | ||
+ | python3 / | ||
+ | |||
+ | -n #slices | ||
+ | -v TR in seconds | ||
+ | |||
+ | </ | ||
+ | |||
+ | RetroTS will produce " | ||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | |||
+ | ====== CIGAL pdigm specific ====== | ||
+ | [[biac: | ||
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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- | ===== 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 ). | ||
biac/analysis/physiological.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1