Hello FSLers,
I have a question about data formats and nifti headers. I have a series of image files, that when opened in fslview using the fsl3.3 release, there is no problem (meaning that they look like they are supposed to and don't give me any errors when opening them). However, when I open the same images in fsl4.0 using fslview (or any other fsl program) I get the following error
++ WARNING: nifti_read_buffer(__filename.nii.gz__):
data bytes needed = 633600
data bytes input = 633596
number missing = 4 (set to 0)
And in fslview it appears to be slightly moved over relative to where it should be and was in fsl3.3.
I found that a solution to this problem was to convert to AFNI and then back to FSL (now the FSL4.0) using the following commands.
#Convert to AFNI
>3dcopy filename.nii.gz test
#Convert the AFNI back to NIFTI
>3dAFNItoNIFTI test+orig. test
When I use the 3dcopy command, I get the following warning message
++ Program 3dcopy: AFNI version=AFNI_2006_12_22_0933 [32-bit]
qform not present, sform used.
sform was not exact, and the worst axis is
6.626820 degrees from plumb.
However, my new test.nii now looks just fine when I open it up in fslview from the fsl4.0 release and gives me no errors. I believe this fixes the problem ok, but I'm not sure what causes the error or if it creates some other problems for me with these images. Am I creating more problems with this solution? Where does the problem come from?
Thanks for any help,
Jason