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Hi, This config file is the same as what we use. When you say that it "failed for two images" - did this include the ones you sent me? It is hard to figure out what is wrong if the same images are failing for you but working for me. If you are talking about different images then it would be helpful if you could upload these for us. All the best, Mark On 14 Aug 2012, at 16:37, Marina Shpaner wrote: > Hello Mark, > > Thank you for looking into this. It actually failed for two images (and I tried both GUI and scripts), and I don't think there was a typo in the naming judging from the log. Perhaps there is something wrong with the configuration file I'm using, copied below? > > Thank you for your help. > -Marina > > # name of reference image > # --ref=/usr/local/fsl/data/standard/MNI152_T1_2mm.nii.gz > --ref=MNI152_T1_2mm > # 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_2mm_brain_mask_dil > # 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=4,4,2,2,1,1 > # 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 > # Weigth of membrane energy 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 > # Apply the mask if set, default 1 (true) > --applyrefmask=1,1,1,1,1,1 > # 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 >