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biac:analysis:physiological [2011/11/03 18:41] petty [AFNI] |
biac:analysis:physiological [2013/04/02 19:40] petty [FSL Feat] |
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Currently this assumes that you have recorded your physiological responses through Cigal. | Currently this assumes that you have recorded your physiological responses through Cigal. | ||
- | There' | + | ===== physio_run.py ===== |
+ | There is currently | ||
- | This tool uses various fields from the bxh and pdigm file to output " | + | < |
+ | physio_run.py --help | ||
+ | </ | ||
+ | |||
+ | < | ||
+ | Usage: | ||
+ | physio_run.py / | ||
+ | |||
+ | Program to produce formatted physiological data: | ||
+ | Data will be corrected and recreated from the pdigm file based on information from run data | ||
+ | BXH and PDIGM required | ||
+ | OUTPUTPREFIX is the prefix for the physio-corrected output | ||
+ | FORMAT: what pipeline to use, only supports ' | ||
+ | |||
+ | Options: | ||
+ | -h, --help | ||
+ | -f string, --format=string | ||
+ | output format ( afni ) | ||
+ | </ | ||
+ | |||
+ | '' | ||
+ | |||
+ | The outputs will be OUTPUTPREFIX.bxh, | ||
+ | |||
+ | ===== physio_create.py ===== | ||
+ | |||
+ | The underlying tool used by '' | ||
+ | |||
+ | This tool uses various fields from the bxh and pdigm file to output " | ||
The python tool will call cigal functions directly to do the corrections, | The python tool will call cigal functions directly to do the corrections, | ||
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- fsl = cardio, | - fsl = cardio, | ||
- npm = time, | - npm = time, | ||
- | - afni = cardiac.txt, | + | - afni = cardiac.txt, |
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</ | </ | ||
- | ===== AFNI ===== | + | ===== AFNI details |
+ | |||
+ | This section details the steps that the tool '' | ||
Create the AFNI formated physiological text data. | Create the AFNI formated physiological text data. | ||
<code bash> | <code bash> | ||
- | This would create my " | + | This would create my " |
- | + | ||
- | Now set-up build the regressors | + | |
<code matlab> | <code matlab> | ||
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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) | ||
</ | </ | ||
- | The output will be **" | + | The output |
Convert your data to 4D nifti if you haven' | Convert your data to 4D nifti if you haven' | ||
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<code bash> | <code bash> | ||
- | There will be a resulting folder with all the afni data inside. | + | There will be a resulting folder with all the afni data inside. |
<code bash> | <code bash> | ||
#convert afni to nii, create bxh | #convert afni to nii, create bxh | ||
- | 3dAFNItoNIFTI | + | bxh2analyze --niigz -s 12345.results/ |
- | fslwrapbxh pb02.12345.r01.ricor.BRIK | + | |
</ | </ | ||
Run the resting state pipeline: | Run the resting state pipeline: | ||
- | <code bash> | + | <code bash> |
- | + | ||
- | + | ||
- | ===== 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 ). | ||