If you want to re-generate a valid BXH for the corrected data, you can generate a new BXH and merge in the original infoīxh_merge. The bottom two images are the mean functional image of a series uncorrected, then corrected by the topup results. The top two images are an example of the polarity images after correction, which is not necessary. Readout = ((echospacing/sensefactor) * (acquisitionmatrix * (percentsampling/100))) / 1e6 If your functional data and PEPOLAR images have the same sensefactor, this compensation is not needed. You will need to divide the echospacing by the sensefactor from your BXH header of the functional run. You can create an additional acq_params file with a modified readout time to help prevent over correction. If you have the scenario where the functional data was acquired with acceleration, but the PEPOLAR images were not. Inindex references the “regular” image index from your acq_params.txt file, which is the same phase encode direction of your functional runsĪpplytopup -imain=./bia6_00186_008_01.nii.gz -inindex=1 -method=jac -datain=acq_params.txt -topup=rs_topup -out=run008 -verboseĪpplytopup -imain=./bia6_00186_009_01.nii.gz -inindex=1 -method=jac -datain=acq_params.txt -topup=rs_topup -out=run009 -verboseĪpplytopup -imain=./bia6_00186_010_01.nii.gz -inindex=1 -method=jac -datain=acq_params.txt -topup=rs_topup -out=run010 -verbose Reverse will be “-1” in the acq_params.txt and regular will be “1” Below shows the PEPOLAR images in red/blue on top of a mean functional. Take note of the eyeballs being crushed in for AP and stretched out for PA. Here is a rough guide to help with inspection. we aren't provided enough information in the metadata to give an entry into the BXH file ( yet ). Unfortunately at this point the polarity of the images will have to be determined from visual inspection. most all scans will be 4Īsset_R_factor = the reciprocal of the first value of dcm tag (0043,1083) Round_factor = 4 if partial fourier ( PFF is in scanoptions ), 2 if full fourier. The readout time in seconds for the parameter file will be:įor singleband images : readout = (echospacing * (acquisitionmatrix * (percentsampling/100))) / 1e6Įchospacing in the BXH header is in microsecondsįor mutli-band images the readout calculation is more complex: readout = ( ( ceil ((1/Round_factor) * AcquisitionMatrixPE / Asset_R_factor ) * Round_factor) - 1 ) * EchoSpacing * 0.000001ĪcquisitionMatrixPE = the acquisition size of the data ( acquisitionmatrix ) You need to calculate readout time in seconds of the PEPOLAR images ( the physical time it takes to get the acquisition matrix of a single slice ) and get the polarity direction ( phase encode direction ). You can grab relevant info to create the acq_params.txt files from your XML header. Have you observed this compatibility issue before? Is there any way to change that number so that FSL sees the correct number of volumes? Is this an FSL issue and thus must be posted there? Although they'd probably reply to me it is an AFNI issue, and so forth.There will be two series of single timepoint EPI images. I would like to do a subsequent analysis in FSL (dual regression with randomise), but FSL gives me problems because it identifies as if there were only one volume. Selecting the volumes is easier and quicker in AFNI with 3dbucket, so I did as follows:ģdbucket -prefix melodic_IC_ 'melodic_IC.nii.gz'Īlthough 3dinfo indicates a correct number of volumes (as a summary):įslinfo indicates that there is only one volume in the 4th dimension!! I've done a Group ICA analysis with MELODIC in FSL, and I wanted to create a bucket with a subset of the maps of the components of interest. I have an issue of compatibility between AFNI and FSL.
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