Hi Mark,
Whilst I did find a similar error message reported in the archive, our
situation is a little different from the one reported earlier, so here
goes:
We have been processing functional MRI data on two systems, MacOSX and
Linux (running Ubuntu). FSL software versions are both 4.1 (2008).
Setting up feat, the preprocessing steps were identical and involve B0
corrections (one processing stream involved FNIRT, and one FLIRT at
the registration step, which is the only difference in the processing
path). During the fieldmap correction step, when invoking fslmaths,
the processing run under Linux gives us the following error, that the
Mac OSX processing does not give us:
WARNING:: Inconsistent orientations for individual images in pipeline!
Will use voxel-based orientation which is probably incorrect
- *PLEASE CHECK*!
The images printed in the report.html of the unwarping step do seem
fine to me in both cases.
Upon checking the header information of the fslmaths input files,
there do seem to be differences in pixel dimensions, which may well
underlie the error/warning reporting, but I am not sure why that is an
issue on one system but not the other (suggesting software
differences?)?
Relatedly, if we need to worry about these pixeldimension differences,
how best to fix these?
Below the header information of the different files (processed under
Linux for the most part), in case this is useful information. Happy to
send the log-file along if useful.
thanks in advance for any pointers,
Carien
fslinfo ../../../fieldmap/ar04_fm_rad_per_sec.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 0.4880000055
cal_max 1275.8230
cal_min -1277.0702
file_type NIFTI-1+
fslinfo FM_UD_fmap.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo ../../../fieldmap/T1_ar04_fm_rad_per_sec.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 0.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo FM_UD_fmap_mag.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 0.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo FM_UD_fmap_mag_brain_mask
data_type INT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 8
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 1.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
fslinfo FM_UD_fmap_mag_brain_mask_inv
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000042915
pixdim4 0.4880000055
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
Why is the 4rth pixeldim more than half in brain_mask_inv from the
brain_mask when all that is done is /usr/local/fsl/bin/fslmaths
FM_UD_fmap -abs -bin -mas FM_UD_fmap_mag_brain_mask -mul -1 -add 1
-bin FM_UD_fmap_mag_brain_mask_inv ??
Finally, the example func has been copied into a file called EF_D_etc
and has the following info:
fslinfo EF_D_example_func.nii.gz
data_type FLOAT32
dim1 64
dim2 64
dim3 30
dim4 1
datatype 16
pixdim1 3.0000000000
pixdim2 3.0000000000
pixdim3 5.0000000000
pixdim4 2.0000000000
cal_max 0.0000
cal_min 0.0000
file_type NIFTI-1+
--
Centre for Integrative Neuroscience and Neurodynamics
School of Psychology and Clinical Language Sciences
University of Reading
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