# Population\_template FOV **URL:** \ **Category:** Uncategorized\ **Created:** [October 18, 2020, 12:14pm UTC](https://community.mrtrix.org/t/population-template-fov/4199 "2020-10-18T12:14:07Z")\ **Posts on this page:** 6\ **Page:** 1
**Author:** ![mblesac](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mblesac/32/2210_2.png) [@mblesac](https://community.mrtrix.org/u/mblesac)\ **Post date:** [October 18, 2020, 12:14pm UTC](https://community.mrtrix.org/t/population-template-fov/4199/1 "2020-10-18T12:14:07Z")
Dear Mrtrix experts, I’m running population\_template on my neonatal population, the first average looks reasonable: ![image](https://community.mrtrix.org/uploads/default/original/2X/9/915365f55a189e2dafe79588df76758c1d740756.png) however the template is outside the FOV, I found that the error is in the first rigid registration: ![image](https://community.mrtrix.org/uploads/default/original/2X/d/db7101f2c8fa17b74e40e3c823cfbbc5f505e747.png) And both overlaid: ![image](https://community.mrtrix.org/uploads/default/original/2X/b/b18e540424bcc8de7a7047952ab3ffb7699e11bb.png) Is there any way to optimize this first step in the population\_template script? Thanks in advance. Best regards, Manuel ---
**Author:** ![maxpietsch](https://community.mrtrix.org/user_avatar/community.mrtrix.org/maxpietsch/32/25_2.png) [@maxpietsch](https://community.mrtrix.org/u/maxpietsch)\ **Post date:** [October 21, 2020, 8:30am UTC](https://community.mrtrix.org/t/population-template-fov/4199/2 "2020-10-21T08:30:42Z")
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`? ---
**Author:** ![mblesac](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mblesac/32/2210_2.png) [@mblesac](https://community.mrtrix.org/u/mblesac)\ **Post date:** [October 21, 2020, 2:11pm UTC](https://community.mrtrix.org/t/population-template-fov/4199/3 "2020-10-21T14:11:10Z")
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: ```auto ************************************************ 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: ```auto 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_name 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 aux_file ``` 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, Manuel ---
**Author:** ![maxpietsch](https://community.mrtrix.org/user_avatar/community.mrtrix.org/maxpietsch/32/25_2.png) [@maxpietsch](https://community.mrtrix.org/u/maxpietsch)\ **Post date:** [October 22, 2020, 5:04am UTC](https://community.mrtrix.org/t/population-template-fov/4199/4 "2020-10-22T05:04:13Z")
Just to rule out a viewer problem, have you looked at the images with mrview? Which of the following images is cropped? ```auto 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 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](https://github.com/MRtrix3/mrtrix3/blob/994abf7433b9ce92a4e017ce353b5f6c492d04b6/bin/population_template#L1217) by ```auto 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. ---
**Author:** ![mblesac](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mblesac/32/2210_2.png) [@mblesac](https://community.mrtrix.org/u/mblesac)\ **Post date:** [October 22, 2020, 8:07am UTC](https://community.mrtrix.org/t/population-template-fov/4199/5 "2020-10-22T08:07:05Z")
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: ```auto 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, Manuel ---
**Author:** ![mblesac](https://community.mrtrix.org/user_avatar/community.mrtrix.org/mblesac/32/2210_2.png) [@mblesac](https://community.mrtrix.org/u/mblesac)\ **Post date:** [October 22, 2020, 11:35am UTC](https://community.mrtrix.org/t/population-template-fov/4199/6 "2020-10-22T11:35:17Z")
Hi Max, After modifing the line as you suggested and running the following command: `population_template out.mif -mask -type rigid -scratch regtest -nocleanup` I obtained the following template ![image](https://community.mrtrix.org/uploads/default/original/2X/3/3f1b41ced55bf9467e9849adad74e5c921402230.png) Do you want to take a look to the `linear_transforms_*` folders? You can see the files [here](https://datasync.ed.ac.uk/index.php/s/NGWZeWa1jauCNDm) where the modified are the ones with the modified version of population\_template (the password is template). Thanks in advance. Best regards, Manuel