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how to use hippunfold with CBRAIN Web-based Platform

Open rzxxzxy opened this issue 11 months ago • 5 comments

When I select the task parameters, this problem appears. I don’t know where I went wrong? image

rzxxzxy avatar Jan 02 '25 08:01 rzxxzxy

@akhanf dear professor Ali R Khan, please help me, thanks!

rzxxzxy avatar Jan 02 '25 08:01 rzxxzxy

Looks like you are passing it a nifti when you need to pass it the subject directory (sub-01) that contains anat/sub-01_T1w.nii

akhanf avatar Jan 02 '25 12:01 akhanf

But I don not know how to pass a folder, I can only select a file and not a folder. image

rzxxzxy avatar Jan 02 '25 12:01 rzxxzxy

@akhanf dear professor Ali R Khan, I am sorry to bother you again, but I still failed. Could you please record a video with a sample? Than you very much!

rzxxzxy avatar Jan 04 '25 09:01 rzxxzxy

In this example, you need to either:

  • create a folder structure online on CBRAINs, so hippunfold can accept a BIDS folder as input OR
  • use the --path_T1w to point directly to the nii file (e.g. hippunfold . output participant --path_T1w sub-{subject}_T1w.nii.gz). I believe this will show up as optional arguments in CBRAINs, but its been a while since I've used it

jordandekraker avatar Jan 05 '25 15:01 jordandekraker