Unknown parameter -rI

[ines-c]

I downloaded the cbica:captk image (version 1.9.rc), and I believe there may be an issue in the Preprocessing module.

I tried running the registration example provided in your documentation using the following command:

/work/CaPTk/bin/Preprocessing
-i /data/data_captk_tests/_0001/T2W_TSE_corrected.nii.gz
-o /data/data_captk_tests/_0001/T2W_TSE_corrected.nii.gz
-reg Deformable
-rFI /data/data_captk/_0001/T1CE_to_SRI.nii.gz
-rIA /data/data_captk_tests/_0001/T2W_TSE.mat
However, I encountered the following error:

Unknown parameter -rI
Something went wrong when calling Greedy Affine.

Could you please help me understand what might be going wrong or guide me on how to resolve this?

Thank you in advance for your support!

[hugocarlesso]

Did you manage to find a fix? I am dealing with the same error.

[ines-c]

@hugocarlesso
Yes, I think so. The issue seems to come from the Preprocessing module in the cbica/captk:1.9rc image not recognizing the -rFI / -rIA parameters (they trigger the “Unknown parameter -rI” error).

Instead of using the Preprocessing wrapper, I switched to calling greedy directly and handled the registration + transform chaining manually. That resolved the issue and produced the expected outputs.

So it looks like either the documentation is outdated or those parameters aren’t supported in that version of CaPTk. IDK

---

look at this example
/work/CaPTk/bin/greedy -d 3
-rf /path/to/atlas.nii.gz
-ri LINEAR
-rm /path/to/T1ce.nii.gz /path/to/T1ce_in_atlas.nii.gz
-r /path/to/T1ce_to_atlas.mat