Running FSLv6.0.0 on RHEL v7.3
Hoping someone can suggest a command line solution for bedpostx to handle eddy_openmp outputs. It seems as if bedpostx still expects "legacy" eddy_correct outputs (e.g. data.nii.gz, .bvecs, .bvals, nodif_brain_mask.nii.gz). Since eddy provides freedom to write --out and generates .eddy_rotated_bvecs and incorporates a my_hifi_b0_brain_mask.nii.gz (if one follows the FSL eddy tutorial), the rigid legacy filename expectations of bedpostx seem to be outdated. I can work around this by running a script to copy my eddy_openmp outputs to a new directory (e.g. <post_eddy>) and then rename the eddy_openmp output files to conform with the "legacy" filenames probtrackx expects (which is what I did during the eddy patch releases)...
I like eddy and would like to embrace him with commandline bedpostx where I can specify my eddy_openmp outputs (dtifit permitted me to do this)
I can't seem to overcome the expectations of bedpostx to have rigid "legacy" filenames.
Am I missing something?
Many Thanks,
Jenifer
[jjuranek@localhost post_eddy]$ bedpostx /home/jjuranek/fsl/subjects/dti/test --data eddy_corrected_64dir.nii.gz --mask my_hifi_b0_brain_mask.nii.gz --bvecs eddy_corrected_64dir.eddy_rotated_bvecs --bvals 64dir.bval --nf=2 --fudge=1 --bi=1000
subjectdir is /home/jjuranek/fsl/subjects/dti/test
/home/jjuranek/fsl/subjects/dti/test/bvecs not found
[jjuranek@localhost post_eddy]$ bedpostx
Usage: bedpostx <subject directory> [options]
expects to find bvals and bvecs in subject directory
expects to find data and nodif_brain_mask in subject directory
expects to find grad_dev in subject directory, if -g is set
options (old syntax)
-n (number of fibres per voxel, default 3)
-w (ARD weight, more weight means less secondary fibres per voxel, default 1)
-b (burnin period, default 1000)
-j (number of jumps, default 1250)
-s (sample every, default 25)
-model (Deconvolution model. 1: with sticks, 2: with sticks with a range of diffusivities (default), 3: with zeppelins)
-g (consider gradient nonlinearities, default off)
ALTERNATIVELY: you can pass on xfibres options onto directly bedpostx
For example: bedpostx <subject directory> --noard --cnonlinear
Type 'xfibres --help' for a list of available options
Default options will be bedpostx default (see above), and not xfibres default.
Note: Use EITHER old OR new syntax.
[jjuranek@localhost post_eddy]$ xfibres --help
Part of FSL (ID: 6.0.0)
xfibres
Usage:
xfibres --help (for list of options)
Compulsory arguments (You MUST set one or more of):
-k,--data,--datafile data file
-m,--mask, --maskfile mask file
-r,--bvecs b vectors file
-b,--bvals b values file
Optional arguments (You may optionally specify one or more of):
-V,--verbose switch on diagnostic messages
-h,--help display this message
--ld,--logdir log directory (default is logdir)
--forcedir Use the actual directory name given - i.e. don't add + to make a new directory
--nf,--nfibres Maximum number of fibres to fit in each voxel (default 1)
--model Which model to use. 1=deconv. with sticks (default). 2=deconv. with sticks and a range of diffusivities. 3=deconv. with zeppelins
--fudge ARD fudge factor
--nj,--njumps Num of jumps to be made by MCMC (default is 5000)
--bi,--burnin Total num of jumps at start of MCMC to be discarded (default is 0)
--bn,--burnin_noard num of burnin jumps before the ard is imposed (default is 0)
--se,--sampleevery Num of jumps for each sample (MCMC) (default is 1)
--upe,--updateproposalevery Num of jumps for each update to the proposal density std (MCMC) (default is 40)
--seed seed for pseudo random number generator
--noard Turn ARD off on all fibres
--allard Turn ARD on on all fibres
--nospat Initialise with tensor, not spatially
--nonlinear Initialise with nonlinear fitting
--cnonlinear Initialise with constrained nonlinear fitting
--rician Use Rician noise modelling
--f0 Add to the model an unattenuated signal compartment
--ardf0 Use ard on f0
--Rmean Set the prior mean for R of model 3 (default:0.13- Must be<0.5)
--Rstd Set the prior standard deviation for R of model 3 (default:0.03)
[jjuranek@localhost post_eddy]$
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