Dear Shaun and other FSL experts,
Thanks for that - I think the epi_reg that I used for B0 to T1 was already using BBR?
There is still one more thing that I want to try - I suspect that one of the reasons why using the FA map to FSL_HCP1065_FA_1mm is working better on the non inferior-frontal area is because of a resolution of 1mm warp, in contrast to the MNI152 2mm template.
Therefore I am trying to "hack" into the configuration file of T1_2_MNI152_2mm.cnf file to make my command work for a 1mm resolution warp instead:
fnirt --in=T1 --ref=/usr/local/fsl/data/standard/MNI152_T1_1mm --fout=T1_to_MNI_nonlin_field --iout=T1_to_MNI_nonlin --config= T1_2_MNI152_2mm.cnf --aff=T1_to_MNI_lin.mat
I just wonder if anyone case done something similar (I know it will take longer time but I just want to try) and can give me comments on how I should edit the cnf file? I have tried the make the following changes in brackets but the results was quite bizarre and not making sense at all..with frequent warning of "Jacobian not within prescribed range"
# name of reference image
# --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz
--ref=/usr/local/fsl/data/standard/MNI152_T1_1mm.nii.gz (changed)
# name of file with mask in reference space
# --refmask=/usr/local/fsl/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz
--refmask=MNI152_T1_1mm_brain_mask_dil (changed to a 1mm mask)
# If =1, use implicit masking based on value in --ref image. Default =1
--imprefm=1
# If =1, use implicit masking based on value in --in image, Default =1
--impinm=1
# Value to mask out in --ref image. Default =0.0
--imprefval=0
# Value to mask out in --in image. Default =0.0
--impinval=0
# sub-sampling scheme, default 4,2,1,1
--subsamp=8,8,4,4,2,2 (changed according to suggestion https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=fsl;7acee487.0905)
# Max # of non-linear iterations, default 5,5,5,5
--miter=5,5,5,5
# FWHM (in mm) of gaussian smoothing kernel for input volume, default 6,4,2,2
--infwhm=12,6,2,2
# FWHM (in mm) of gaussian smoothing kernel for ref volume, default 4,2,0,0
--reffwhm=12,6,2,2
# Weigth of membrane energy regularisation, default depending on --ssqlambda and --regmod switches. See user documetation.
--lambda=300,75,30,30
# Estimate intensity-mapping if set, deafult 1 (true)
--estint=1,1,1,0
# Apply the mask if set, default 1 (true)
--applyrefmask=1,1,1,1
# Apply the mask if set, default 1 (true)
--applyinmask=1
# (approximate) resolution (in mm) of warp basis in x-, y- and z-direction, default 10,10,10
--warpres=10,10,10
# If set (=1), lambda is weighted by current ssq, default 1
--ssqlambda=1
# Model for regularisation of warp-field [membrane_energy bending_energy], default bending_energy
--regmod=bending_energy
# Model for intensity-mapping [none global_linear global_non_linear local_linear global_non_linear_with_bias local_non_linear]
--intmod=global_non_linear_with_bias
# Order of poynomial for mapping intensities, default 5
--intorder=5
# Resolution (in mm) of bias-field modelling local intensities, default 50,50,50
--biasres=50,50,50
# Weight of regularisation for bias-field, default 10000
--biaslambda=10000
# If =1, ref image is used to calculate derivatives. Default =0
--refderiv=0
again thank you for any help at all!!
Oscar
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