Open shnizzedy opened 1 year ago
This may actually be a design decision:
Looking at the code where [this command is generated]https://github.com/FCP-INDI/C-PAC/blob/v1.8.4/CPAC/image_utils/spatial_smoothing.py) and called https://github.com/FCP-INDI/C-PAC/blob/12c4f74a3cfeb544239e34301853b90b34d7edc1/CPAC/pipeline/engine.py#L700-L737, only derivatives (the ones with “Yes” under “To Smooth” in this table, like ALFF, ReHo) are smoothed in C-PAC, and space-template_desc-preproc_bold isn’t one of those.
― @shnizzedy
the mask on which the smoothing is supposed to occur is the same mask across subjects…..
― A.D.M.
Ah! That might be the answer as to why this step doesn't happen in the participant-level pipeline! So we’d just need to swap in the correct mask.
― @shnizzedy
in older versions of C-PAC (at least for v1.7.0, which is the one we have used for other pipelines) the functional to standard images were also smoothed and saved when the pipeline config file had the section for spatial smoothing enabled.
― @ppombosegura
Discovered by @ppombosegura
Describe the bug
No
desc-sm
files are appearing in the output directory, and the-NN_smooth 74
option for3dSkullStrip
is the only smoothing shown inpypeline.log
withpost_processing, spatial_smoothing, output: [smoothed, nonsmoothed]
Custom pipeline configuration
Expected behavior
Both smoothed and nonsmoothed outputs are generated, and clearly differentiated in their filenames
Acceptance criteria
C-PAC version
v1.8.4 & v1.8.5
Container platform
Docker
Additional context
I created a https://github.com/FCP-INDI/C-PAC/labels/forking label in case any of these issues share a cause.