Possible error with ASLCONTEXT_TSV_NOT_CONSISTENT

[witherscp]

Hi,

I have used dcm2niix to convert my ASL data collected with a 3T GE Discovery 750 scanner from dicom to BIDS format. As has been previously explained, the GE ASL sequences are unusual in that there is a deltam sequence computed in k-space and a m0scan. Both of these sequences are present within the same folder of dcm files. After running dcm2niix, I used bids-validator to ensure that the outputs were correct, but I encountered the same problem that other users have experienced. Can we possibly resolve the source of this problem?

With my example dataset, I ran nifti_tool -disp_hdr -infiles sub-p260_ses-research_asl.nii.gz. This is the output:

N-1 header file 'sub-p260_ses-research_asl.nii.gz', num_fields = 43

all fields:
  name                offset  nvals  values
  ------------------- ------  -----  ------
  sizeof_hdr             0      1    348
  data_type              4     10    
  db_name               14     18    
  extents               32      1    0
  session_error         36      1    0
  regular               38      1    r
  dim_info              39      1    57
  dim                   40      8    3 128 128 40 1 1 1 1
  intent_p1             56      1    0.0
  intent_p2             60      1    0.0
  intent_p3             64      1    0.0
  intent_code           68      1    0
  datatype              70      1    4
  bitpix                72      1    16
  slice_start           74      1    0
  pixdim                76      8    1.0 1.7266 1.7266 3.0 4.705 0.0 0.0 0.0
  vox_offset           108      1    352.0
  scl_slope            112      1    1.0
  scl_inter            116      1    0.0
  slice_end            120      1    0
  slice_code           122      1    0
  xyzt_units           123      1    10
  cal_max              124      1    0.0
  cal_min              128      1    0.0
  slice_duration       132      1    0.0
  toffset              136      1    0.0
  glmax                140      1    0
  glmin                144      1    0
  descrip              148     80    TE=11;Time=160846.000
  aux_file             228     24    
  qform_code           252      1    1
  sform_code           254      1    1
  quatern_b            256      1    0.0
  quatern_c            260      1    0.0
  quatern_d            264      1    0.0
  qoffset_x            268      1    -112.38221
  qoffset_y            272      1    -89.158218
  qoffset_z            276      1    -56.318401
  srow_x               280      4    1.7266 0.0 0.0 -112.38221
  srow_y               296      4    0.0 1.7266 0.0 -89.158218
  srow_z               312      4    0.0 0.0 3.0 -56.318401
  intent_name          328     16    
  magic                344      4    n+1

My aslcontext.tsv file looks like this:

volume_type
deltam

I notice a few things. First of all, there are three dimensions and the fourth one is set to 1. This means that there shouldn't be an error of a mismatch between dim[4] and the number of rows in the tsv file. Something weird seems to be going on though because the fourth pixdim is 4.705. I tried using fslchpixdim sub-p260_ses-research_asl.nii.gz 1.726600 1.726600 3 0 to change the fourth pixel dimension to 0 manually, but this did not resolve the error.

Do you have any suggestions?

Thanks!
Price

[effigies]

If I'm reading this and the linked threads correctly, this is a 4D _asl file with a single volume. In which case dim[0] should be 4, not 3. That would be consistent with pixdim[4] having a non-trivial value, and should then allow you to compare the 4th entry in the shape tuple with the length of your volume_type column.

There's probably an easy command-line tool to reshape a data array, but you could do something like this in Python:

import nibabel as nb
img = nb.load(in_fname)
print(img.shape)  # (128, 128, 40)
reshaped = img.slicer[:, :, :, None]
print(img.shape)  # (128, 128, 40, 1)
reshaped.to_filename(out_fname)

[witherscp]

This fixed it! Thanks so much for the help.