Population_template FOV

Dear Mrtrix experts,

I’m running population_template on my neonatal population, the first average looks reasonable:


however the template is outside the FOV, I found that the error is in the first rigid registration:


And both overlaid:


Is there any way to optimize this first step in the population_template script? Thanks in advance.

Best regards,


Hi Manuel,

This looks like an issue with the initial alignment (-inital_alignment) before any linear registration is run but given your description I am having trouble seeing what exactly the issue might be. One option is that none of your masks cover the entire brain (check with mrview image -roi.load mask). Otherwise, to debug this, could you check which files in the scratch directory are fine and what the first cropped image is in initial_template*.mif linear_template*.mif?

Hi Max,

Thanks for your reply. I tried changing the -initial_alignment to robust_mass and the result is the same. I inspected all the masks and they look ok.

These images were converted from dicom to nifti long ago. See attached the outputs from mrinfo and fslhd for one subject:

Here the output of mrinfo:

Image name:          "7005/7005-dwi_den_eddy_bias_res.nii.gz"
  Dimensions:        256 x 256 x 100 x 75
  Voxel size:        1 x 1 x 1 x 1
  Data strides:      [ -1 2 3 4 ]
  Format:            NIfTI-1.1 (GZip compressed)
  Data type:         32 bit float (little endian)
  Intensity scaling: offset = 0, multiplier = 1
  Transform:                    1           0           0      -254.5
                               -0           1           0        -0.5
                               -0           0           1        -0.5
  comments:          5.0.11
  mrtrix_version:    3.0_RC3-15-g9494da8d

and the output from fslhd:

filename	7005/7005-dwi_den_eddy_bias_res.nii.gz

sizeof_hdr	348
data_type	FLOAT32
dim0		4
dim1		256
dim2		256
dim3		100
dim4		75
dim5		1
dim6		1
dim7		1
vox_units	mm
time_units	s
datatype	16
nbyper		4
bitpix		32
pixdim0		-1.000000
pixdim1		1.000000
pixdim2		1.000000
pixdim3		1.000000
pixdim4		1.000000
pixdim5		0.000000
pixdim6		0.000000
pixdim7		0.000000
vox_offset	352
cal_max		0.000000
cal_min		0.000000
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
toffset		0.000000
intent		Unknown
intent_code	0
intent_p1	0.000000
intent_p2	0.000000
intent_p3	0.000000
qform_name	Scanner Anat
qform_code	1
qto_xyz:1	-1.000000 0.000000 -0.000000 0.500000 
qto_xyz:2	0.000000 1.000000 -0.000000 -0.500000 
qto_xyz:3	0.000000 0.000000 1.000000 -0.500000 
qto_xyz:4	0.000000 0.000000 0.000000 1.000000 
qform_xorient	Right-to-Left
qform_yorient	Posterior-to-Anterior
qform_zorient	Inferior-to-Superior
sform_name	Scanner Anat
sform_code	1
sto_xyz:1	-1.000000 0.000000 0.000000 0.500000 
sto_xyz:2	0.000000 1.000000 0.000000 -0.500000 
sto_xyz:3	0.000000 0.000000 1.000000 -0.500000 
sto_xyz:4	0.000000 0.000000 0.000000 1.000000 
sform_xorient	Right-to-Left
sform_yorient	Posterior-to-Anterior
sform_zorient	Inferior-to-Superior
file_type	NIFTI-1+
file_code	1
descrip		MRtrix version: 3.0_RC3-15-g9494da8d

I find strange the last column of the qform to be 0 0 0 1 (in the not resampled image) but I don’t know if this is related at all with the issue.

Best regards,


Just to rule out a viewer problem, have you looked at the images with mrview? Which of the following images is cropped?

population_template <odfs> out.mif -mask <masks> -type rigid -rigid_scale 0.3,0.4 -scratch regtest -nocleanup
cd regtest
mrview -load initial_template_c0.mif -colourmap 4  -load linear_template00_c0.mif -colourmap 4 -load linear_template01_c0.mif -colourmap 4 -mode 2

I don’t think I can figure out what’s going on with the header information only. If you can reproduce the problem with a few images and are able to share these and the command options that’d probably the fastest way to get to the bottom of this.

Otherwise, I’d modify population_template and replace this line by

      average_inv = None

and check if the problem goes away. If so I’d be interested in the content of the linear_transforms_* folders in the scratch dir generated with this modification.

Hi Max,

I can see the same problem in two different versions of the software, the 3.0_RC3-15-g9494da8d and the 3.0.0

The FOD images look right in mrview

When I run this:

population_template out.mif -mask -type rigid -rigid_scale 0.3,0.4 -scratch regtest -nocleanup
cd regtest
mrview -load initial_template_c0.mif -colourmap 4 -load linear_template00_c0.mif -colourmap 4 -load linear_template01_c0.mif -colourmap 4 -mode 2

I find the following error:

population_template: Generating a population-average template from 20 input images
population_template: SH Series detected, performing FOD registration in contrast: regtest/fod_input
population_template: [ERROR] Unhandled Python exception:
population_template: [ERROR]   AssertionError:
population_template: [ERROR] Traceback:
population_template: [ERROR]   /EBC/local/MRtrix3_stable/mrtrix3/bin/population_template:823 (in execute())
population_template: [ERROR]     assert len(linear_lmax) == len(linear_niter)

I’ll try to find a way to share the images.

Best regards,


Hi Max,

After modifing the line as you suggested and running the following command:

population_template <odfs> out.mif -mask <masks> -type rigid -scratch regtest -nocleanup

I obtained the following template

Do you want to take a look to the linear_transforms_* folders? You can see the files here where the modified are the ones with the modified version of population_template (the password is template). Thanks in advance.

Best regards,