biac:analysis:topup_correction
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biac:analysis:topup_correction [2019/02/22 17:41] – [Prepare your input datasets] cmp12 | biac:analysis:topup_correction [2019/09/04 20:25] – cmp12 | ||
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There will be two series of single timepoint EPI images. | There will be two series of single timepoint EPI images. | ||
- | You need to calculate readout time in seconds ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ). | + | You need to calculate readout time in seconds |
the readout time in seconds for the parameter file will be: | the readout time in seconds for the parameter file will be: | ||
Line 15: | Line 15: | ||
</ | </ | ||
+ | unfortunately at this point the polarity of the images will have to be determined from visual inspection. we aren't provided enough information in the metadata to give an entry into the BXH file ( yet ). | ||
+ | |||
+ | Here is a rough guide to help with inspection. | ||
+ | {{: | ||
- | the polarity for the entry will have to be determined from the **seriesdescription**, | ||
reverse will be " | reverse will be " | ||
Line 62: | Line 65: | ||
applytopup --imain=../ | applytopup --imain=../ | ||
applytopup --imain=../ | applytopup --imain=../ | ||
+ | </ | ||
+ | |||
+ | If you have the scenario where the functional data was acquired with acceleration, | ||
+ | |||
+ | < | ||
+ | echospacing in the BXH header is in microseconds | ||
</ | </ | ||
Line 205: | Line 214: | ||
For scenario 1, create your blip up / blip down B0 data the same way as above. | For scenario 1, create your blip up / blip down B0 data the same way as above. | ||
< | < | ||
- | bxhselect --timeselect 0 bi | + | bxhselect --timeselect 0 bia6_00197_012.bxh bu |
- | a6_00197_012.bxh bu | + | |
bxhselect --timeselect 0 bia6_00197_013.bxh bd | bxhselect --timeselect 0 bia6_00197_013.bxh bd | ||
fslmerge -t bud bu.nii.gz bd.nii.gz | fslmerge -t bud bu.nii.gz bd.nii.gz |
biac/analysis/topup_correction.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1