One word of advice: Try converting using dcm2ii which is part of "mricron" (the replacement for mricro).
http://www.sph.sc.edu/comd/rorden/mricron/dcm2nii.html
It automatically creates a 4D NIFTI file. Also has other useful
features such as recursive action, anonimization, and others. Even
calculates an expected number of files (based on number of slices and
acquisition). and reports when the number of files does not match the
prediction.
Besides being a possible improvement to your process it can
give you a second source for a the same data in 4D NIFTI format, which
you can check with Feat and Melodic.
I am having problems opening 4D nii.gz epi files with Feat and Melodic.
The images were collected on a Seimens scanner in NEMA format.
They have been converted to 3D hdr/img volume files using MRIcro, then
converted to individual 3D volume nii.gz files using fslchfiletype and then
merged into a single 4D nii.gz file using fslmerge.
I can open and view the file using Fslview, but neither Melodic or Feat
will recognize the file (not able to determine number of volumes within or
run from gui).
The header info is as follows:
sizeof_hdr 348
data_type INT16
dim0 4
dim1 128
dim2 128
dim3 19
dim4 35
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 1.8799999952
pixdim2 1.8799999952
pixdim3 6.0000000000
pixdim4 1.0000000000
pixdim5 0.0000000000
pixdim6 0.0000000000
pixdim7 0.0000000000
vox_offset 352
cal_max 2851.0000
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 Unknown
qform_code 0
qto_xyz:1 1.880000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 1.880000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 6.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL4.0
aux_file
Does anyone know what the problem might be?
Thanks
Tony