MouseIn template issue

[AnriiGegliuk]

What happened?

Dear all, I am trying to use MouseIn templates to get a brain mask on BL6 mouse, and I got the following error.

What command did you use?

input_files = ['path']
output = 'path'

be_wf = init_rodent_brain_extraction_wf(template_id="MouseIn",  mri_scheme='T2w', output_dir=output_dir)
be_wf.inputs.inputnode.in_files = input_files

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
Cell In[13], line 1
----> 1 be_wf = init_rodent_brain_extraction_wf(template_id="MouseIn",  mri_scheme='T2w', output_dir=output_dir)
      2 be_wf.inputs.inputnode.in_files = input_files

File ~/mri_course/workflow/brain_extraction.py:683, in init_rodent_brain_extraction_wf(ants_affine_init, factor, arc, step, grid, debug, interim_checkpoints, mem_gb, mri_scheme, name, omp_nthreads, output_dir, template_id, template_specs, use_float)
    681 tpl_target_path = get_template(template_id, suffix=mri_scheme, **template_specs,)
    682 if not tpl_target_path:
--> 683     raise RuntimeError(
    684         f"An instance of template <tpl-{template_id}> with MR scheme '{mri_scheme}'"
    685         " could not be found."
    686     )
    688 tpl_brainmask_path = get_template(
    689     template_id,
    690     atlas=None,
   (...)
    701     **template_specs,
    702 )
    704 tpl_regmask_path = get_template(
    705     template_id,
    706     atlas=None,
   (...)
    709     **template_specs,
    710 )

RuntimeError: An instance of template <tpl-MouseIn> with MR scheme 'T2w' could not be found. 


I have tried T1 + suphixes for templates inside the tpl-MouseIn. 


I understand that there is no T2w inside tpl-MouseIn:

➜  tpl-MouseIn tree                                                                 base
.
├── CHANGES
├── LICENSE
├── template_description.json
├── tpl-MouseIn_res-1_T1map.nii.gz
├── tpl-MouseIn_res-1_UNIT1.nii.gz
├── tpl-MouseIn_res-1_atlas-CCFv3_desc-DC_dseg.nii.gz
├── tpl-MouseIn_res-1_desc-CSF_mask.nii.gz
├── tpl-MouseIn_res-1_desc-CSF_probseg.nii.gz
├── tpl-MouseIn_res-1_desc-GM_probseg.nii.gz
├── tpl-MouseIn_res-1_desc-WM_probseg.nii.gz
├── tpl-MouseIn_res-1_desc-brain_mask.nii.gz
├── tpl-MouseIn_res-1_inv-1_MP2RAGE.nii.gz
├── tpl-MouseIn_res-1_inv-2_MP2RAGE.nii.gz
├── tpl-MouseIn_res-2_desc-brain_T1map.nii.gz
└── tpl-MouseIn_res-2_desc-brain_UNIT1.nii.gz


So I am just wandering what can I do? If there is a way to load our templates for registation and mask? Or there is some parameters I can change? Apologies if I am missing something obvious.

What version of the software are you running?

up to date one

How are you running this software?

Local installation ("bare-metal")

Is your data BIDS valid?

No

Are you reusing any previously computed results?

Work directory

Please copy and paste any relevant log output.

No response

Additional information / screenshots

this is just an ouput which Fischer344 template gave me

[eilidhmacnicol]

Thank you for bringing this to our attention.

There needs to be some logic to look for T1map as a pseudo-T2w image, as the contrasts are similar (although not identical). This should be a fairly straight forward fix, but might need a little optimization in the case that the T1map registration parameters need some tweaking.