I have noticed a bug in seeds to targets mode of probtrackx:

The seeds_to_targets files do not have proper NIFTI headers.  When running something like:

probtrackx --seed=<image.nii.gz> --targetmasks=<targetlist.txt> --dir=<results folder> --samples=<merged> --mask=<nodif_brain_mask> --stop=<stop mask> --xfm=<xfm> --loopcheck --cthr=0.2 --nsteps=2000 --steplength=0.5 --nsamples=25000 --fibthresh=0.05 --opd --os2t --fibst=1 --modeuler –forcedir

There is output a fdt_paths.nii.gz, which contains all of the samples that were sent out, and a number of seeds to targets files as expected.  The fdt_paths.nii.gz has an appropriate header that matches the seed’s header, e.g.:

filename       fdt_paths.nii.gz

sizeof_hdr     348

data_type      INT32

dim0           3

dim1           58

dim2           69

dim3           58

dim4           1

dim5           1

dim6           1

dim7           1

vox_units      mm

time_units     s

datatype       8

nbyper         4

bitpix         32

pixdim0        0.0000000000

pixdim1        3.0000000000

pixdim2        3.0000000000

pixdim3        3.0000000000

pixdim4        1.0000000000

pixdim5        0.0000000000

pixdim6        0.0000000000

pixdim7        0.0000000000

vox_offset     352

cal_max        4.0000

cal_min        0.0000

scl_slope      0.000000

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     Scanner Anat

qform_code     1

qto_xyz:1      3.000000  0.000000  0.000000  -84.500000

qto_xyz:2      0.000000  3.000000  0.000000  -123.500000

qto_xyz:3      0.000000  0.000000  3.000000  -74.500000

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     Scanner Anat

sform_code     1

sto_xyz:1      3.000000  0.000000  0.000000  -84.500000

sto_xyz:2      0.000000  3.000000  0.000000  -123.500000

sto_xyz:3      0.000000  0.000000  3.000000  -74.500000

sto_xyz:4      0.000000  0.000000  0.000000  1.000000

sform_xorient  Left-to-Right

sform_yorient  Posterior-to-Anterior

sform_zorient  Inferior-to-Superior

file_type      NIFTI-1+

file_code      1

descrip        FSL4.0

aux_file      

The seeds_to_targets files do not have proper headers, e.g.:

filename       seeds_to_2.nii.gz

sizeof_hdr     348

data_type      FLOAT32

dim0           3

dim1           58

dim2           69

dim3           58

dim4           1

dim5           1

dim6           1

dim7           1

vox_units      mm

time_units     s

datatype       16

nbyper         4

bitpix         32

pixdim0        0.0000000000

pixdim1        1.0000000000

pixdim2        1.0000000000

pixdim3        1.0000000000

pixdim4        1.0000000000

pixdim5        0.0000000000

pixdim6        0.0000000000

pixdim7        0.0000000000

vox_offset     352

cal_max        0.0000

cal_min        0.0000

scl_slope      0.000000

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      1.000000  0.000000  0.000000  0.000000

qto_xyz:2      0.000000  1.000000  0.000000  0.000000

qto_xyz:3      0.000000  0.000000  1.000000  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      

Basically, the pixel dimensions are not set, and neither are the qforms or sforms. 

Thanks,

Matt.