User Tools
biac:analysis:topup_correction
Differences
This shows you the differences between two versions of the page.
| Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
|
biac:analysis:topup_correction [2019/02/21 19:33] cmp12 |
biac:analysis:topup_correction [2019/02/22 17:41] cmp12 [Prepare your input datasets] |
||
|---|---|---|---|
| Line 192: | Line 192: | ||
| there are 2 scenarios that typically apply here | there are 2 scenarios that typically apply here | ||
| - | 1) a short acquisition with RPE B0s | + | 1) DWI and a short acquisition with RPE B0s |
| - | 2) an entire | + | 2) 2 entire |
| In both scenarios it is important to create your data with normal phase encoding direction first, followed by reversed. | In both scenarios it is important to create your data with normal phase encoding direction first, followed by reversed. | ||
| Line 200: | Line 200: | ||
| ==== Prepare your input datasets ==== | ==== Prepare your input datasets ==== | ||
| + | |||
| + | Specify that a set of images (typically b=0 volumes) will be provided for use in inhomogeneity field estimation only | ||
| 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 bia6_00197_012.bxh bu | + | bxhselect --timeselect 0 bi |
| + | 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 | ||
| Line 226: | Line 229: | ||
| </ | </ | ||
| - | The last step seems redundant, but there is an issue with how mrtrix3 tools are handling the multi-shell GE data produced on our scanners. | + | The last step seems redundant, but there is an issue with how mrtrix3 tools are handling the multi-shell GE data produced on our scanners. |
| ==== Run dwipreproc -rpe_pair ==== | ==== Run dwipreproc -rpe_pair ==== | ||
| Line 233: | Line 236: | ||
| < | < | ||
| - | dwipreproc | + | dwipre |
| + | proc dwi.mif dwi_corr.mif -rpe_pair -se_epi bud.nii.gz -pe_dir AP -readout_time 0.10656 | ||
| -rpe_pair specifies you're providing a pair of B0s ( regular, reversed ) | -rpe_pair specifies you're providing a pair of B0s ( regular, reversed ) | ||
| Line 250: | Line 254: | ||
| ===== Scenario 2 ===== | ===== Scenario 2 ===== | ||
| - | You have an entire acquisition with the same gradient table as your DWI sequence, but with reverse phase encoding. | + | You have an entire acquisition with the same gradient table as your DWI sequence, but with reverse phase encoding. This information will be used to perform a recombination of image volumes (each pair of volumes with the same b-vector but different phase encoding directions will be combined together into a single volume). |
| Calculate the readout time in the same way as above | Calculate the readout time in the same way as above | ||
| Line 260: | Line 264: | ||
| < | < | ||
| #concat the 2 series ( regular, reversed ) | #concat the 2 series ( regular, reversed ) | ||
| - | bxh_concat | + | bxh_concat |
| + | 7_LAS.bxh bia6_00260_008_LAS.bxh both | ||
| #extract the gradients | #extract the gradients | ||
| - | extractdiffdirs --fsl both bvecs bvals | + | extractdiffdirs --fsl both.bxh bvecs bvals |
| #convert to mif | #convert to mif | ||
| Line 285: | Line 290: | ||
| dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug | dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug | ||
| - | -rpe_all signals that you've replicated | + | -rpe_all signals that you've replicated |
| + | A | ||
| + | LL the directions with a rpe acquisition | ||
| -pe_dir is the phase encode direction of your regular acquisition | -pe_dir is the phase encode direction of your regular acquisition | ||
| -readout_time from above | -readout_time from above | ||
| </ | </ | ||
| + | |||
| + | {{ : | ||
biac/analysis/topup_correction.txt · Last modified: 2023/02/23 18:43 (external edit)
Page Tools
Except where otherwise noted, content on this wiki is licensed under the following license: CC Attribution-Share Alike 4.0 International
