# Population template FOV cropped issue **URL:** \ **Category:** Uncategorized\ **Tags:** error, mrview, fba, registration\ **Created:** [April 14, 2022, 9:44pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681 "2022-04-14T21:44:24Z")\ **Posts on this page:** 16\ **Page:** 1
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 14, 2022, 9:44pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/1 "2022-04-14T21:44:24Z")
Hi MRtrixers! So far I’ve been following along the FBA multi-tissue CSD tutorial without issue ([Fibre density and cross-section - Multi-tissue CSD — MRtrix 3.0 documentation](https://mrtrix.readthedocs.io/en/latest/fixel_based_analysis/mt_fibre_density_cross-section.html)) - until running the population\_template command and having the occipital cortex cropped out of the template: ![population_template_firstattempt_FOVissue.PNG](https://community.mrtrix.org/uploads/default/original/2X/a/a7e50961fe1f94f53c28a97b244f780527ba3eae.jpeg) I checked all the masks to see if there was an issue with coverage - but the masks look fine. I saw a similar issue in the thread here: [Population\_template FOV](https://community.mrtrix.org/t/population-template-fov/4199) . I’m going to try re-running the command with the flag -initial\_alignment robust\_mass option to see if that fixes the issue - but in the meantime I have 2 questions: 1. How can I save the debug output to a file for later viewing? I tried: `population_template /study_template/fod_input -mask_dir /study_template/mask_input /study_template/wmfod_template.mif -voxel_size 1.25 -initial_alignment robust_mass -template_mask study_template/template_mask.mif -force -debug -nocleanup -scratch /data/AS_HC_Study/FBA/study_template/scratch > /study_template/debug.txt ` but the STDOUT still goes to the terminal. 1. Anything else I should try looking at to troubleshoot while this runs? Thanks for your time, Ariana ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 16, 2022, 12:50pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/2 "2022-04-16T12:50:16Z")
Hi again, re-running with -initial\_alignment robust\_mass completed, but unfortunately did not fix the issue. From the other thread, please see below the requested images of the initial template and first linear template that was cropped (which in my case, was the very first linear template) : ![crop](https://community.mrtrix.org/uploads/default/original/2X/a/aa4f5f8e013bf4b0ebf1be4e28a4aab35102d3ac.png) ---
**Author:** ![Jiaying\_Zhang](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jiaying_zhang/32/3083_2.png) [@Jiaying\_Zhang](https://community.mrtrix.org/u/Jiaying_Zhang)\ **Post date:** [April 17, 2022, 3:58pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/3 "2022-04-17T15:58:39Z")
Hi Ariana, I happened to have a similar issue earlier and am happy to share with you how to solve it. What I found was that some subject had different q-form and s-form in the header of the nifti images from others. So once you identify which subjects have this issue, then you can rerun your analysis without those subjects. Then I think you will find the cropped issue is gone. Hope it helps. Jiaying Zhang ---
**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:** [April 18, 2022, 9:33am UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/4 "2022-04-18T09:33:10Z")
Hi, I solved the problem in the past following Max’s suggestion about modifying the line in population template: > 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. I hope this helps. Best regards, Manuel ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 18, 2022, 6:26pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/5 "2022-04-18T18:26:37Z")
Hi Jiaying Zhang, Thanks for sharing this - I wasn’t aware there was the possibility for different q/s form headers (I’m new to neuroimaging - lots to learn lol). I’ll check this out, though ideally I’d like to be able to keep the subjects I had chosen for the template. Is this I guess only an issue for forming the template - but not an issue for registering subjects to the template later down the line? ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 18, 2022, 6:29pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/6 "2022-04-18T18:29:56Z")
Hi Manuel, Thanks for sharing this again. I saw your post / this solution, but posted again for the following reasons: 1. I saw you were using neonatal data, and didn’t see anyone else with adult data with a similar issue, so I was concerned maybe something was weird about my data and didn’t want to change source code before trying other possible work arounds (assuming most people work with adult imaging data) 2. I’m not sure what changing that line of code changes exactly for the formation of the template - Max asked to look at the output afterwards but the thread ended there. I’d be interested to hear what changing this line changes about the population template creation? Ariana ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 20, 2022, 6:15pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/7 "2022-04-20T18:15:36Z")
I changed the source code as Manuel suggested, and got what appears to be a proper population template. If it’s possible to explain what changing this line of code altered, I’d appreciate it - thanks! ![pop_temp_sourceedit](https://community.mrtrix.org/uploads/default/original/2X/8/805c720b9c19a07dd0d7088a21d80e39df1854e7.png) ---
**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:** [April 21, 2022, 10:30am UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/8 "2022-04-21T10:30:25Z")
Setting `average_inv = None` results in deactivating the drift correction that prevents scaling, rotation or translation between template iterations in the linear registration steps. The template might take longer to converge and might be overall different in shape and location due to the lack of this linear correction. I’ve created an issue [population\_template: bogus average space · Issue #2467 · MRtrix3/mrtrix3 · GitHub](https://github.com/MRtrix3/mrtrix3/issues/2467) for this bug. If you’re willing to help us find the cause for this issue, could you please have a look at the instructions there? ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [April 21, 2022, 1:33pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/9 "2022-04-21T13:33:00Z")
Will do! Thanks a lot for the explanation ---
**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:** [April 26, 2022, 8:51pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/11 "2022-04-26T20:51:54Z")
@abesik has sent me some data to investigate (thanks!) … but I haven’t had time to look into it. Soothsaying, sform vs qform issues are quite unlikely the culprit here. You might not encounter the issue after resetting the NIfTI transforms but I think that would be a side effect. (And you’d need to make sure no unexpected side effects creep in: [NIfTI transform ambiguity](https://community.mrtrix.org/t/nifti-transform-ambiguity/2254)). ---
**Author:** ![Jiaying\_Zhang](https://community.mrtrix.org/user_avatar/community.mrtrix.org/jiaying_zhang/32/3083_2.png) [@Jiaying\_Zhang](https://community.mrtrix.org/u/Jiaying_Zhang)\ **Post date:** [April 29, 2022, 7:53pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/12 "2022-04-29T19:53:34Z")
Ah I see. Sure, just let us know when you figure out this problem.Thanks! Jiaying ---
**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:** [May 1, 2022, 4:20pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/13 "2022-05-01T16:20:56Z")
The issue was a bug in the drift correction to which resetting the centre of the input images is a sensible workaround. If you want, you can [try](https://community.mrtrix.org/t/testing-different-code-branches/2570) the fix [proposed](https://github.com/MRtrix3/mrtrix3/pull/2471) in the `population_template_space_init_drift_fix` branch which should solve the FOV issue. Note that this fix does change the behaviour of `population_template` and is not yet part of the master code branch and it might change before it makes it there. To check the effect of the drift correction on the template shape, you could add the option `-linear_no_drift_correction`. ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [May 2, 2022, 4:58pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/14 "2022-05-02T16:58:40Z")
Thanks a lot for taking the time to figure this out, Max! Really appreciate it. Just to clarify… to check the effect of drift correction on the template shape, I should add the option `-linear_no_drift_correction` to the proposed fixed version of the command and compare that to running the fixed command without this option, as opposed to comparing it to the original command with this option? Is this the equivalent to modifying the original code to set average\_inv = none or is this different? Within your git fix, you mention: " deactivating drift correction via `-linear_no_drift_correction` leads to visible distortion in the affine levels that increase with the number of levels iterations." Sorry… I am not familiar with all the math that’s going on here - but does this mean it is best not to deactivate drift correction for the actual population template that is to be used in analysis (but it is useful just as a way to examine how this new modification to the code impacts the template shape?) ---
**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:** [May 3, 2022, 2:43pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/15 "2022-05-03T14:43:53Z")
The drift correction is supposed to prevent the template from gradually changing its size or overall shape over iterations. We do that by (approximately) preserving the average transformation at each linear registration stage. The “new” drift correction is very similar to the old version, except that it does not factor out the average transformation after initialisation (which is fixed and therefore cannot drift). I’d leave this feature active except for in edge cases (i.e. debugging or when dealing with registration outliers). `-linear_no_drift_correction` is a new option added in the `population_template_space_init_drift_fix` branch that deactivates this feature – similar to setting `average_inv = None`. (However, there were other changes to the code in that branch that affect the initialisation so you’d get different results compared to the `master` branch code if you use any of the robust initialisation methods.) I just mentioned this option in case you ran `population_template` with the `average_inv = None` and would like to see the effect of deactivating the drift correction on the template shape. In my data, the effect was clearly visible but even if this is the case for your data as well, the overall template shape might not matter for your analysis. Besides, there are multiple ways of defining an average affine transformation so there is no universal ground truth appearance. ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [May 4, 2022, 3:24pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/16 "2022-05-04T15:24:05Z")
Thank you for explaining that! Unfortunately I seem to be running into issues running this new command… ![error](https://community.mrtrix.org/uploads/default/original/2X/f/ff77f8790553d20a11de591696bc97961b298872.png) I have tried using the -force option - still gave the error. I tried to switch the directories I saved the template into / also changed the name of the output file and still got the error. The command I used was: `/home/abesik-local/mrtrix3_testbranch/bin/population_template /data/AS_HC_Study/FBA/study_template/fod_input -mask_dir /data/AS_HC_Study/FBA/study_template/mask_input /data/study_template_testbranch/wmfod_template_testbranch.mif -voxel_size 1.25 -force` (I’ve been using bash instead of the python command). I am running it on the same participants I included when I ran the population\_template command before - is there somehow a file somewhere that needs to be deleted before I can run this again? ---
**Author:** ![abesik](https://community.mrtrix.org/letter_avatar_proxy/v4/letter/a/e274bd/32.png) [@abesik](https://community.mrtrix.org/u/abesik)\ **Post date:** [May 10, 2022, 5:18pm UTC](https://community.mrtrix.org/t/population-template-fov-cropped-issue/5681/17 "2022-05-10T17:18:59Z")
Hey everyone, to finish up this thread… the issue I had above was a result of needing to fully build the testbranch of MRtrix so that other commands (eg mrgrid) required for population\_template to run properly are compiled, as opposed to just building the particular population\_template command (which is actually a script and so isn’t compiled anyway). The wiki page for testing branch code has been edited to reflect this - Thanks Max for solving this! Just wanted to share the end result of the three different population template commands… ![poptemplate](https://community.mrtrix.org/uploads/default/original/2X/e/ecf863e898494b9b24b4612da2ade1874427c294.gif) Top left, wmfod\_template is the edited original source code per above to deactivate linear drift correction (`average_inv = None`). Top right, wmfod\_template\_testbranch is the result of the testbranch `population_template_space_init_drift_fix` code. Bottom left, wmfod\_template\_testbranch\_noL is the result of the testbranch population\_template\_space\_init\_drift\_fix code but with` -linear_no_drift_correction` The two template with no linear drift correction are very similar, but not the same, as Max mentioned they would be. The size and shape of the testbranch template is different than those with no linear drift correction. Thanks again Max for your help with this / everyone else for commenting. Cheers!