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Software fsl/6.0.7.7 appears to havesrc/fsl-topup/ instead of src/topup. But freesurfer (trac-prepro and nifti1.py) still uses the folder src/topup.
/bin/trac-preproc: if ($dob0 > 1) then # B0 inhomogeneities: with topup
/bin/trac-preproc: echo "ERROR: Cannot correct B0 distortions with topup" |& tee -a $LF
/bin/trac-preproc: # If image has an odd dimension, must turn off topup subsampling :/
t/bin/trac-preproc: set cnf = $FSLDIR/src/topup/flirtsch/b02b0.cnf
/bin/trac-preproc: set cmd = (cp -p $FSLDIR/src/topup/flirtsch/b02b0.cnf $dwidir)
/bin/trac-preproc: set cmd = topup
/bin/trac-preproc: set cmd = ($cmd --out=$dwidir/topup)
/bin/trac-preproc: set cmd = ($cmd --iout=$dwidir/lowb_topup.nii.gz)
/bin/trac-preproc: set cmd = applytopup
/bin/trac-preproc: set cmd = ($cmd --topup=$dwidir/topup)
/bin/trac-preproc: else # No topup, only combine runs
/bin/trac-preproc: if ($dob0 > 1) then # Have b=0 images unwarped by topup
/bin/trac-preproc: set lowbase = $dwidir/lowb_topup
/bin/trac-preproc: if ($dob0 > 1) then # Use previously run topup output
/bin/trac-preproc: set cmd = ($cmd --topup=$dwidir/topup)
/bin/trac-preproc: if ($dob0 > 1) then # Apply unwarping from topup
/bin/trac-preproc: set cmd = applytopup
/bin/trac-preproc: set cmd = ($cmd --topup=$dwidir/topup)
/python/lib/python3.8/site-packages/nibabel/__pycache__/nifti1.cpython-38.pyc: binary file matches
/python/lib/python3.8/site-packages/nibabel/nifti1.py: # ($FSLDIR/topup/topup_file_io.h:104)
/python/lib/python3.8/site-packages/nibabel/nifti1.py: (2016, 'topup cubic spline coef ', (), 'FSL_TOPUP_CUBIC_SPLINE_COEFFICIENTS'),
/python/lib/python3.8/site-packages/nibabel/nifti1.py: (2017, 'topup quad spline coef', (), 'FSL_TOPUP_QUADRATIC_SPLINE_COEFFICIENTS'),
/python/lib/python3.8/site-packages/nibabel/nifti1.py: (2018, 'topup field', (), 'FSL_TOPUP_FIELD'),
Can fsl change the folder topup to fsl-topup?
The text was updated successfully, but these errors were encountered:
Software
fsl/6.0.7.7
appears to havesrc/fsl-topup/
instead ofsrc/topup
. Butfreesurfer
(trac-prepro and nifti1.py) still uses the foldersrc/topup
.Can
fsl
change the foldertopup
tofsl-topup
?The text was updated successfully, but these errors were encountered: