Hi,
I have recently started working on FNIRT and I am having trouble
registering T1 structural images of higher resolution. The program
works great for medium resolution images (256X256X110) but inspite of
some different permutations like changing the --subsamp=8,8,4,4,2,2 ,
I am not able to configure the settings properly for high resolution
images (512x512x110). I am following the method given in the examples
usage on the FNIRT help website and am using teh reference
MNI152_T1_1mm. Unfortunately the computer I am running the program on,
has limited memory (2GB => executing time ~ 1.5hrs) so I cannot try a
lot of different settings.
Could you from your experience please guide me and provide possible
settings for 512x512x110 images. I have copied the log file from a
trial run which did not work for me. Thank you for your help.
Sincerely,
Jayanth Kolar
# name of reference image
--ref=/usr/local/fsl/data/standard/MNI152_T1_1mm
# name of input image
--in=E15778S26
# name of file containing affine transform
--aff=E15778S26_brain_affine.mat
# name of output file with field coefficients
--cout=E15778S26_nonlinear_transf
# name of file with mask in reference space
--refmask=/usr/local/fsl/data/standard/MNI152_T1_1mm_brain_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
# Max # of non-linear iterations, default 5,5,5,5
--miter=5,5,5,5,5,10
# FWHM (in mm) of gaussian smoothing kernel for input volume, default 6,4,2,2
--infwhm=8,6,5,4.5,3,2
# FWHM (in mm) of gaussian smoothing kernel for ref volume, default 4,2,0,0
--reffwhm=8,6,5,4,2,0
# Weight of regularisation, default depending on --ssqlambda and
--regmod switches. See user documetation.
--lambda=300,150,100,50,40,30
# Estimate intensity-mapping if set, deafult 1 (true)
--estint=1,1,1,1,1,0
# (approximate) resolution (in mm) of warp basis in x-, y- and
z-direction, default 10,10,10
--warpres=10,10,10
# Order of spline, 2->Qadratic spline, 3->Cubic spline. Default=3
--splineorder=3
# If set (=1), lambda is weighted by current ssq, default 1
--ssqlambda=1
# Allowed range of Jacobian determinants, default 0.01,100.0
--jacrange=0.01,100
# 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
# Precision for representing Hessian, double or float. Default double
--numprec=double
# If =1, ref image is used to calculate derivatives. Default =0
--refderiv=0
--
Jayanth Kolar
Graduate Research Assistant
Physiological Imaging and Modeling Lab
University of Illinois at Chicago
Chicago IL - 60607
1-408-398-0097
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