---
# System prepended metadata

title: Untitled

---

🐛 Rodent data registered incorrectly

### Describe the bug

Related to #1532
C-PAC rodent nuisance regression residuals seem to be in a different space than those from our rodent pipeline benchmark

### To reproduce

Run C-PAC with `--preconfig rodent` and compare outputs to benchmark

### Expected behavior

Outputs are in the same space

### Acceptance Criteria

- [ ] outputs appear to be in the same space

### Screenshots


### C-PAC version
v1.8.3

### Container platform
Docker

### Docker and/or Singularity version(s)

_No response_

### Additional context

Discovered while testing #1656.

Benchmark scripts on our server in `/data3/cnl/rodent/Marco_rodent_code`.

Maybe I'm just not seeing where this is applied, but I wonder if this is related to the different-space issue for rodents:
https://github.com/FCP-INDI/C-PAC/blob/7d3b973637d57975ea125601bf38cb20ecf1a374/CPAC/resources/configs/pipeline_config_rodent.yml#L142-L144
I don't know what this template is, I don't think it's included the C-PAC image, and I don't see where C-PAC tries to use it, but the comment says
> EPI template for direct functional-to-template registration
>           # (bypassing coregistration and the anatomical-to-template transforms)

Looking at `/data3/cnl/agutierrez/issue_runs/Rodent_noSeg_test/test9_warning_message/rodent_pipeline/working/cpac_sub-ag150519a_ses-1/ANTS_bold_to_EPI-template_75/cpac_sub-ag150519a_ses-1/anat_mni_ants_register/_scan_rest/calc_ants_warp/_report/report.rst` I see in the inputs
```
* interp : LanczosWindowedSinc
* moving_brain : /output/working/cpac_sub-ag150519a_ses-1/_scan_rest/func_mean_42/ag150519a_10_xan_pcp_trm_500_chopped_despiked_calc_resample_tstat.nii.gz
* moving_mask : /output/working/cpac_sub-ag150519a_ses-1/_scan_rest/erode_one_voxel_50/ag150519a_10_xan_pcp_trm_500_chopped_despiked_calc_resample_mcf_tstat_maths_restore_brain_mask_ero.nii.gz
* moving_skull : /output/working/cpac_sub-ag150519a_ses-1/_scan_rest/func_mean_42/ag150519a_10_xan_pcp_trm_500_chopped_despiked_calc_resample_tstat.nii.gz
* reference_brain : /output/working/fcp-indi/resources/cpac/resources/epi_hbn.nii.gz
* reference_mask : <undefined>
* reference_skull : /output/working/fcp-indi/resources/cpac/resources/epi_hbn.nii.gz
* reg_with_skull : 1
```
The template seems to be coming from https://github.com/FCP-INDI/C-PAC/blob/2fb2eba4ee242f68988187b2cd0a2e4b91af7e73/dev/docker_data/default_pipeline.yml#L806-L808 instead.


Co-authored-by: @shnizzedy (if Amy posts)
Co-authored-by: @amygutierrez (if Jon posts)
