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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