This parameters (--dfout and --jacout) in topup

wly · October 28, 2023, 3:24am

What are the use of this parameters (–dfout and --jacout) in topup, please? I didn’t find anything about it on the official website or in the help.

jsein · October 28, 2023, 11:28am

Hi,

--dfout: warp field

--jacout : : output Jacobian image (of the TOPUP warp field)

Additionally you can also get:

--rbmout : MotionMatrix

I found this information in this code (line 299)

github.com

Washington-University/HCPpipelines/blob/master/global/scripts/TopupPreprocessingAll.sh

#!/bin/bash 

# Requirements for this script
#  installed versions of: FSL, gradunwarp (HCP version)
#  environment: HCPPIPEDIR, FSLDIR, HCPPIPEDIR_Global, PATH for gradient_unwarp.py

# ------------------------------------------------------------------------------
#  Verify required environment variables are set
# ------------------------------------------------------------------------------

if [ -z "${HCPPIPEDIR}" ]; then
	echo "$(basename ${0}): ABORTING: HCPPIPEDIR environment variable must be set"
	exit 1
else
	echo "$(basename ${0}): HCPPIPEDIR: ${HCPPIPEDIR}"
fi

if [ -z "${FSLDIR}" ]; then
	echo "$(basename ${0}): ABORTING: FSLDIR environment variable must be set"
	exit 1

This file has been truncated. show original

By the way, for FSL specific question, you could also ask the FSL forum when you can get direct answers from the FSL developers:

https://www.jiscmail.ac.uk/cgi-bin/webadmin?A0=fsl

wly · October 28, 2023, 12:14pm

Thanks for the guidance, what is the difference among --fout, --dfout and --jacout?

jsein · October 28, 2023, 12:47pm

My general understanding is that the fieldmap is the estimation of the B0 field deviation (usually in Hertz), the warping field is the deformation field that needs to be applied to the data depending on the fieldmap and the data acquisition parameters. The Jacobian modulation serves to adjust the intensities of voxels that have been stretched or compressed.

wly · October 28, 2023, 3:40pm

I understand, thanks for the guidance.