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Mathilde-16 / STOP_MS_data

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Unclear how the SPINEPS batch is supposed to be used-- and possible redundancy #15

Closed jcohenadad closed 3 months ago

jcohenadad commented 3 months ago

There are two batch scripts in this repos:

Which one should be run first? Also see #14 about improving the doc.

Also, the SPINEPS batch includes code to segment the cord: https://github.com/Mathilde-16/STOP_MS_data/blob/47faee16341ef70a9ee507c46f1992de082466de/Data_processing/SPINEPS_Vertebral_labeling/Script_SPINEPS.sh#L95

But this is already done here: https://github.com/Mathilde-16/STOP_MS_data/blob/47faee16341ef70a9ee507c46f1992de082466de/Data_processing/ContrastAgnosticSeg_%26_Vertebral-labeling_BIDS-data/Batch_script.sh#L60

There is a lot of redundancy between these two scripts, and clarifying the doc is necessary before others can properly use the code.

Mathilde-16 commented 3 months ago

Hi Julien,

I've just committed and pushed the last version of my script. I also removed the SPINEPS batch script as we are not going to use SPINEPS for the vertebral labeling.

I'll also complete README (issue #14) so that you can understand how to use the script.

Thank you for your help!

jcohenadad commented 3 months ago

@Mathilde-16 please always refer to an issue (eg with 'Fixes #XX') in the commit, so the issue is cross-ref with the commit-- this is good git/github practice

jcohenadad commented 3 months ago

Irrelevant after of https://github.com/Mathilde-16/STOP_MS_data/pull/21