refactor #59
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Hi, I welcome all PRs to the project. I just request that they be
With regards to:
The --dry-run option should suffice there. |
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Could you provide the dry run output for an example run with 1level & 2level, respectively? |
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Here's a dry-run from a 2level run |
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Thanks, I'm running two scans for 1level (I changed the name to avoid confusion of my edits): where: I'll based on the folder structure as above just for convenience. What I wonder is how -j should be chosen. I used 4 since I have a 8-core machine, but ants seems to run with all occupied so it's somewhat slow. Maybe I confuse threads and cores. Could you advise? |
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--local-threads only affects the parallelism for post-processing. For the modelbuild side, antsRegistration uses all available threads and the ANTs scripts haven't really exposed the ability to limit that. |
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I've refactored the first_level part but would like your help with the results part (i.e. line 239 in current code). How should I convert subj_id and visit in the similar line below? first_level
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Hi. I'm not sure where you're going with this right now. Why don't you open a Draft PR to show whats been done so far so we can do a proper code review and discuss the changes and potential future changes. |
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re-running the following with 4x4x4mm input images: where But the following messages showed: Any thoughts? Thank you! |
As the file name of each input file is used in a flat directory structure, you cannot use the same filename for multiple inputs. |
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Hi @gdevenyi , I'm not sure in what stage you'd like me to be involved, but I would like to send you my edited code (mostly minor changes). One function I think would help could be adding a function to generate the command(s) to run, which is included in the edited one I send. I hesitate to PR since I haven't run through the code locally or on cluster (I'll run the registration part on Azure cloud, if you're interested I can share how) . Which email works best for you? Thank you for your effort of building this wonder pipeline!
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