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biac:analysis:physiological [2022/01/20 17:17] cmp12 |
biac:analysis:physiological [2023/02/23 18:43] |
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- | ====== Physiological Correction Methods ====== | ||
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- | ===== Generate resampled TSV from raw GE physio files automatically copied from the scanners | ||
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- | Stock GE physio is hardcoded by GE to be 25Hz for respiration and 100Hz for pulse. | ||
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- | < | ||
- | [cmp12@blade17 20211218_03399]$ / | ||
- | usage: convert_GEphysio.py [-h] --xmlh XMLFNAME [--json JSONFNAME] --physdir | ||
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- | create 100Hz resampled TSV from raw GE physio data | ||
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- | optional arguments: | ||
- | -h, --help | ||
- | --xmlh XMLFNAME | ||
- | --json JSONFNAME | ||
- | --physdir PHYSDIR | ||
- | --bidsout | ||
- | --afnislicetime | ||
- | --delay DELAYTIME | ||
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- | </ | ||
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- | Provide a valid BXH ( and JSON if possible ) and a path to your subject physio folder to convert_GEphysio.py function. | ||
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- | 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. | ||
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- | 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. | ||
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- | < | ||
- | / | ||
- | </ | ||
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- | By default you will get a 100Hz resampled TSV with headers and timing. | ||
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- | The **--bidsout** flag will output a TSV without headers and a BIDS sidecar with appropriate column labels and sampling frequency. | ||
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- | The **--afnislicetime** flag will output two 1D slicetiming files to be used with RetroTS.py and afni_proc.py directly. | ||
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- | === Using afni === | ||
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- | You can create regressors for afni preprocessing from output files above using RetroTS.py | ||
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- | < | ||
- | python3 / | ||
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- | -n #slices | ||
- | -v TR in seconds | ||
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- | </ | ||
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- | RetroTS will produce " | ||
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- | === setup afni despike, retroicor and slicetime correction === | ||
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- | < | ||
- | python3 / | ||
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- | -verb 1 | ||
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- | </ | ||
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- | The above will produce an afni script to throw out 2 timepoints, perform a despike, retroicor physio regression and slice time correction based on the RetroTS output and the physio TSV/json above. | ||
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- | Convert the afni corrected output back to nii.gz to be used for other pre-processing if not using AFNI for all steps | ||
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- | < | ||
- | bxh2analyze --niigz -s pb03.sub-00104_run-4_ricor_phys.r01.tshift+orig.HEAD sub-00104_run-4_physiocorrected | ||
- | </ | ||
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- | ====== CIGAL pdigm specific processing ====== | ||
- | [[biac: | ||