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PennLINC / xcp_d

Post-processing of fMRIPrep, NiBabies, and HCP outputs
https://xcp-d.readthedocs.io
BSD 3-Clause "New" or "Revised" License
79 stars 26 forks source link

FD Thresh arg error #1302

Closed juansanchezpena closed 3 weeks ago

juansanchezpena commented 1 month ago

Summary

xcp_d: error: unrecognized arguments: --fd-thresh 0.3 xcp_d: error: ambiguous option: --f could match --file-format, --fd-thresh, --fd_thresh, --fs-license-file

fd_thresh 0.3 WORKED!

Additional details

What were you trying to do?

fun xcp-d on fmriprep 24.0.1 output:

What did you expect to happen?

conainer launch

What actually happened?

errors above until I used fd_thresh

Reproducing the bug

a " --mode none --participant-label patensasc0085 --input-type fmriprep --file-format cifti --despike  fd_thresh 0.3 -p 36P -m y --motion-filter-type notch --band-stop-min 12 --band-stop-max 18 --output-type interpolated --min-coverage 0"

tsalo commented 1 month ago

Can you share the full command you used that failed, as well as the full command that succeeded?

juansanchezpena commented 1 month ago

Thanks for the prompt reply, I was a bit green in saying it worked. I had an error with the syntax for spike denoise, it seems to be running fine with -f now. Will report if anything changes

From: Taylor Salo @.> Date: Tuesday, October 22, 2024 at 11:26 AM To: PennLINC/xcp_d @.> Cc: Sanchez, Juan (NYSPI) @.>, Author @.> Subject: Re: [PennLINC/xcp_d] xcp_d: error: FD Thresh arg error (Issue #1302)

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Can you share the full command you used that failed, as well as the full command that succeeded?

— Reply to this email directly, view it on GitHubhttps://github.com/PennLINC/xcp_d/issues/1302#issuecomment-2429592366, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARKALFBZIGVYF2LABKLSX63Z4ZVBFAVCNFSM6AAAAABQMXPUWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIMRZGU4TEMZWGY. You are receiving this because you authored the thread.Message ID: @.***>

tsalo commented 3 weeks ago

@juansanchezpena any updates on the --fd-thresh problem? If not, I'll close this issue.

juansanchezpena commented 3 weeks ago

That was a syntax error on my end I apologize

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From: Taylor Salo @.> Sent: Friday, November 1, 2024 10:27:48 AM To: PennLINC/xcp_d @.> Cc: Sanchez, Juan (NYSPI) @.>; Mention @.> Subject: Re: [PennLINC/xcp_d] FD Thresh arg error (Issue #1302)

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@juansanchezpenahttps://github.com/juansanchezpena any updates on the --fd-thresh problem? If not, I'll close this issue.

— Reply to this email directly, view it on GitHubhttps://github.com/PennLINC/xcp_d/issues/1302#issuecomment-2451966025, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ARKALFDDNL46GEDHAYCX64DZ6OFWJAVCNFSM6AAAAABQMXPUWOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDINJRHE3DMMBSGU. You are receiving this because you were mentioned.Message ID: @.***>