Hello Stephen,
It worked everything fine... at least, i didn't receive any error
message from fslmaths and the images looked fine and smoothed. I also
checked the header using fslhd and it seemed right.
Best
Matteo
2014-10-28 12:33 GMT+01:00 Stephen Smith <[log in to unmask]>:
> HI - are you sure the smoothing step output OK - e.g. didn't run out of
> disk/quota/etc?
> Cheers.
>
>
> On 28 Oct 2014, at 11:13, Matteo Diano <[log in to unmask]> wrote:
>
> Dear FSL experts,
> I encountered an "unusual" problem during my spatial-smoothing
> preprocess on the HCP data. I ran Melodic with the FIXed files
> (*clean.nii.gz) and it worked fine; i received all the outputs and it
> was ok. Then I applied the spatial-smoothing using:
>
> fslmaths <input> -kernel gauss 1.2739 -fmean <output>
>
>
> I ran again the same melodic command on the FIXed spatially-smoothed
> data but it printed out continuously this error in the terminal (after
> a while, it aborted itself):
>
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/105014/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/105014/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/105014/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/105014/MNINonLinear/Results/rfMRI_REST2_LR/rfMRI_REST2_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/105014/MNINonLinear/Results/rfMRI_REST2_LR
> done
> Removing mean image ... done
> Individual whitening in a 9 dimensional subspace
>
>
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/113619/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/113619/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> ++ WARNING:
> nifti_read_buffer(/home/fsl/Desktop/insula_HCP/113619/MNINonLinear/Results/rfMRI_REST1_LR/rfMRI_REST1_LR_hp2000_clean_SMOOTH3mm.nii.gz):
> data bytes needed = 3610516
> data bytes input = 0
> number missing = 3610516 (set to 0)
> done
> Removing mean image ... done
> Individual whitening in a 9 dimensional subspace
>
>
> An exception has been thrown
> Runtime error:- detected by Newmat: process fails to converge
>
> MatrixType = Diag # Rows = 1200; # Cols = 1200; lower BW = 0; upper BW = 0
> Trace: Evalue(tql2).
>
> Does anyone know why?
> I am using FSL 5.0.7 on centos 6.5 (16g RAM).
>
> Thank you very much!!!!
> Matteo
>
>
>
> ---------------------------------------------------------------------------
> Stephen M. Smith, Professor of Biomedical Engineering
> Associate Director, Oxford University FMRIB Centre
>
> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK
> +44 (0) 1865 222726 (fax 222717)
> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve
> ---------------------------------------------------------------------------
>
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