Hi,
This warning definitely means that some images are all zeros.
Does example_func look OK in FSLView?
What about prefiltered_func_data if you still have it?
If you don't have it, just use the commands below to regenerate it
and then check.
Having a look at the data in FSLView is the best way to check.
If you cannot see a problem then let us know what type of machine
you are running on and where the data is stored (e.g. NFS mounted
storage, local disk, etc.).
All the best,
Mark
On 2 Jul 2009, at 10:55, Dorit Kliemann wrote:
> Dear all,
>
> I’m currently analyzing some data on first level (single subj/single
> run) with feat and for
> one subj/run I get the following error:
>
>>>>>>>>>>>>
> Prestats
>
> /usr/local/fsl/bin/fslmaths /Users/dorit/SOX_FSL/GAZ_P_22/mri/run2/
> run_swap
> prefiltered_func_data -odt float
> Total original volumes = 180
> Deleting 5 volume(s) - BE WARNED for future analysis!
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data
> prefiltered_func_data 5 175
>
> /usr/local/fsl/bin/fslroi prefiltered_func_data example_func 87 1
>
> /usr/local/fsl/bin/mcflirt -in prefiltered_func_data -out
> prefiltered_func_data_mcf -mats -
> plots -refvol 87 -rmsrel -rmsabs
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
> WARNING::in calculating COG, total = 0.0
>>>>>>>>>>>>>>>
>
> I checked on the forum first but could only find the suggestion that
> maybe the intensity
> level of the image got wrong.
>
> So I followed the advice to check for
>
> fslhd <your4Dinputdata>
> fslstats <your4Dinputdata> -r -R -v -V -c -C
>
>
> (See the output below)
>
> Can anyone help me out interpreting the outputs or does anyone have
> any suggestion for
> what to do with the error?
>
> Thanks for any help,
> Dorit
>
>
> P.S.
> I also rebuilt the original nii from dcms and re-did the whole
> analysis ..still the same
> error...
>
>
>
> Fslhd
>
> [RK3:GAZ_P_22/mri/run2] dorit% fslhd run_swap.nii
> filename run_swap.nii
>
> sizeof_hdr 348
> data_type INT16
> dim0 4
> dim1 104
> dim2 104
> dim3 33
> dim4 180
> dim5 1
> dim6 1
> dim7 1
> vox_units mm
> time_units s
> datatype 4
> nbyper 2
> bitpix 16
> pixdim0 0.0000000000
> pixdim1 2.0000000000
> pixdim2 2.0000000000
> pixdim3 2.0000000000
> pixdim4 2.0000000000
> pixdim5 1.0000000000
> pixdim6 1.0000000000
> pixdim7 1.0000000000
> vox_offset 352
> cal_max 0.0000
> cal_min 0.0000
> scl_slope 1.000000
> scl_inter 0.000000
> phase_dim 0
> freq_dim 0
> slice_dim 0
> slice_name Unknown
> slice_code 0
> slice_start 0
> slice_end 0
> slice_duration 0.000000
> time_offset 0.000000
> intent Unknown
> intent_code 0
> intent_name
> intent_p1 0.000000
> intent_p2 0.000000
> intent_p3 0.000000
> qform_name Scanner Anat
> qform_code 1
> qto_xyz:1 -1.999512 -0.035325 0.026552 102.041588
> qto_xyz:2 -0.038213 1.985662 -0.235979 -84.452980
> qto_xyz:3 0.022193 0.236428 1.985852 -51.885906
> qto_xyz:4 0.000000 0.000000 0.000000 1.000000
> qform_xorient Right-to-Left
> qform_yorient Posterior-to-Anterior
> qform_zorient Inferior-to-Superior
> sform_name Scanner Anat
> sform_code 1
> sto_xyz:1 -1.999512 -0.035334 0.026552 102.042519
> sto_xyz:2 -0.038222 1.985662 -0.235979 -84.452972
> sto_xyz:3 0.022193 0.236429 1.985852 -51.885910
> sto_xyz:4 0.000000 0.000000 0.000000 1.000000
> sform_xorient Right-to-Left
> sform_yorient Posterior-to-Anterior
> sform_zorient Inferior-to-Superior
> file_type NIFTI-1+
> file_code 1
> descrip FSL4.0
> aux_file
>
>
> And fslstats
>
> 0.000000 1148.316040 0.000000 2598.000000 64247040 513976320.000000
> 29077669
> 232621344.000000 -2.626137 -3.139890 -3.594572 51.812481 44.144010
> 18.483029
>
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