biac:analysis:topup_correction
Differences
This shows you the differences between two versions of the page.
Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
biac:analysis:topup_correction [2019/02/21 19:09] – cmp12 | biac:analysis:topup_correction [2021/08/24 18:23] – cmp12 | ||
---|---|---|---|
Line 7: | Line 7: | ||
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: | ||
- | < | + | **For singleband images :** |
+ | < | ||
+ | readout = (echospacing * (acquisitionmatrix[0] * (percentsampling/ | ||
echospacing in the BXH header is in microseconds | echospacing in the BXH header is in microseconds | ||
+ | < | ||
+ | |||
+ | |||
+ | **For mutli-band images the readout calculation is more complex: | ||
+ | < | ||
+ | readout = ( ( ceil ((1/ | ||
+ | |||
+ | EffectiveEchoSpacing = TotalReadoutTime/ | ||
+ | |||
+ | AcquisitionMatrixPE = the acquisition size of the data ( acquisitionmatrix[0] ) | ||
+ | reconMatrixPE = the size of the reconstructed data ( may be different from acquisition because of FFT rules ) | ||
+ | Round_factor = 4 if partial fourier ( PFF is in scanoptions ), 2 if full fourier. | ||
+ | Asset_R_factor = the reciprocal of the first value of dcm tag (0043,1083) | ||
</ | </ | ||
+ | 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 81: | ||
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 180: | Line 205: | ||
[[https:// | [[https:// | ||
+ | |||
+ | If you are running dwidenoise, do it BEFORE dwipreproc. | ||
==== Calculate your readout time ==== | ==== Calculate your readout time ==== | ||
Line 190: | Line 217: | ||
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. | ||
===== Scenario 1 ===== | ===== Scenario 1 ===== | ||
+ | |||
+ | ==== 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. | ||
Line 202: | Line 233: | ||
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 | ||
+ | rm bu.* bd.* | ||
</ | </ | ||
Line 218: | Line 250: | ||
#put THOSE back into the mif header | #put THOSE back into the mif header | ||
mrconvert -grad grads.b dwi.mif dwi.mif -force | mrconvert -grad grads.b dwi.mif dwi.mif -force | ||
+ | |||
</ | </ | ||
- | 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 | + | ==== Run dwipreproc |
Run [[https:// | Run [[https:// | ||
< | < | ||
- | dwipreproc | + | dwifslpreproc |
-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 244: | Line 277: | ||
===== 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 254: | Line 287: | ||
< | < | ||
#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 271: | Line 305: | ||
</ | </ | ||
+ | |||
+ | ==== Run dwipreproc -rpe_all ==== | ||
+ | |||
+ | Run dwipreproc with the " | ||
+ | |||
+ | < | ||
+ | dwipreproc dwi.mif dwi_corr.mif -rpe_all -pe_dir AP -readout_time 0.10656 -debug | ||
+ | |||
+ | - rpe_all signals that you've replicated ALL the directions with a rpe acquisition | ||
+ | - pe_dir is the phase encode direction of your regular acquisition | ||
+ | - readout_time from above | ||
+ | </ | ||
+ | |||
+ | |||
+ | {{ : | ||
biac/analysis/topup_correction.txt · Last modified: 2024/06/21 15:44 by 127.0.0.1