Hello Experts,
I used feat with melodic ICA denoising to create denoised filtered_func_data for 15 subjects, all registed to same standard image. The ran these through FEAT. Now I would like to perform Melodic with Concat-ICA. I think I should do this from the command line to avoid re-registration and such.
When I check the melodic command line options, I don't see the equivalent for resampling resolution, as is seen in the Melodic GUI under the registration to standard image option. Since this was not done in FEAT, I think, I need to figure out how to put it in the melodic command line.
I see the melodic options are as pasted below, am I missing something? Will I end up needed to re-register?
Thank you,
Varina
Usage:
melodic -i <filename> <options>
to run melodic
melodic -i <filename> --ICs=melodic_IC --mix=melodic_mix <options>
to run Mixture Model based inference on estimated ICs
melodic --help
Compulsory arguments (You MUST set one or more of):
-i,--in input file names (either single file name or comma-separated list or text file)
Optional arguments (You may optionally specify one or more of):
-o,--outdir output directory name
-m,--mask file name of mask for thresholding
--nomask switch off masking
--update_mask switch off mask updating
--nobet switch off BET
--bgthreshold brain / non-brain threshold (only if --nobet selected)
-d,--dim dimensionality reduction into #num dimensions (default: automatic estimation)
--dimest use specific dim. estimation technique: lap, bic, mdl, aic, mean (default: lap)
--sep_whiten switch on separate whitening
--sep_vn switch off joined variance nomalisation
-n,--numICs numer of IC's to extract (for deflation approach)
-a,--approach approach for decomposition, 2D: defl, symm (default), 3D: tica (default), concat
--nl nonlinearity: gauss, tanh, pow3, pow4
--vn,--varnorm switch off variance normalisation
--pbsc switch off conversion to percent BOLD signal change
--covarweight voxel-wise weights for the covariance matrix (e.g. segmentation information)
--eps,--epsilon minimum error change
--epsS,--epsilonS minimum error change for rank-1 approximation in TICA
--maxit maximum number of iterations before restart
--maxrestart maximum number of restarts
--mmthresh threshold for Mixture Model based inference
--no_mm switch off mixture modelling on IC maps
--ICs filename of the IC components file for mixture modelling
--mix mixing matrix for mixture modelling / filtering
--smode matrix of session modes for report generation
-f,--filter component numbers to remove
--report generate Melodic web report
--bgimage specify background image for report (default: mean image)
--tr TR in seconds
--logPower calculate log of power for frequency spectrum
--Tdes design matrix across time-domain
--Tcon t-contrast matrix across time-domain
--Sdes design matrix across subject-domain
--Scon t-contrast matrix across subject-domain
--Oall output everything
--Ounmix output unmixing matrix
--Ostats output thresholded maps and probability maps
--Opca output PCA results
--Owhite output whitening/dewhitening matrices
--Oorig output the original ICs
--Omean output mean volume
-v,--verbose switch on diagnostic messages
-V,--version prints version information
--copyright prints copyright information
-h,--help prints this help message
--debug switch on debug messages
--report_maps control string for spatial map images (see slicer)
--remove_deriv removes every second entry in paradigm file (EV derivatives)
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