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Hi,

I have 4D nifti files that were created by concatenating 35 analyze images that were in neurological orientation. This 4D image is also in neurological orientation, but because it was created from the analyze files fsl assumes that the data are stored in radiological orientation. Is there anyway to modify the nifti header so that I can specify the correct orientation resulting in congruent header and data storage orientation? I'd like the keep the data stored in neurological orientation. I'm guessing fslorient -forceneurological doesn't work because the header is missing the fields necessary to encode orientation. 

Currently the header reads as follows:

# FSLEDITHD
# This text file contains the header information for an Analyze or Nifti file
# Simply edit this file then save it and the header will be regenerated
# All lines starting with the hash (#) character, like this line, will be ignored
# Ensure that all lines intended to set values take the form: name = 'value' 
# Note that if the file is Analyze then many settings will be ignored
# Further note that the filetype cannot be changed by this program
#   i.e. changing the nifti_type has no effect
 
<nifti_image
  nifti_type = 'NIFTI-1+'
  image_offset = '352'
  ndim = '4'
  nx = '192'
  ny = '192'
  nz = '55'
  nt = '35'
  dx = '1.25'
  dy = '1.25'
  dz = '2.5'
  dt = '1'
  datatype = '4'
  nbyper = '2'
  byteorder = 'LSB_FIRST'
  scl_slope = '1'
  scl_inter = '0'
  xyz_units = '2'
  time_units = '8'
  descrip = 'FSL4.0'
  num_ext = '0'

# Many fields require codes to be set (e.g. sform_code, qform_code, intent_code)
# Valid values are:
#   sform_code (or qform) :- 0=UNKNOWN, 1=SCANNER_ANAT, 2=ALIGNED_ANAT, 3=TALAIRACH, 4=MNI_152
#   xyz_units :- 1=METER, 2=MM, 3=MICRON 
#   t_units :- 8=SEC, 16=MSEC, 24=USEC, 32=HZ, 40=PPM, 48=RADS
#   intent_code :- 0=NONE, 2=CORRELATION, 3=TTEST, 4=FTEST, 5=ZSCORE, 6=CHISQ, ...
#                  22=PVAL, 23=LOGPVAL, 24=LOG10PVAL, 1001=ESTIMATE, 1002=LABEL (incl masks)
#                  Other codes can be found in the /space/raid/fmri/fsl-4.1.6-centos5_64/src/niftiio/nifti1.h file
 
/>

Thank you,
Angie