something wrong with --labels

[Rachelyolo]

Hi,

I'm new to RABIES and I'm trying to preprocess rat image.

This is the command used. :

Actually, the file path is correct, I don't know why It always showed 'No such file or directory'. Could you help me with this, thank you!

[Gab-D-G]

Hi, a file path does not end with '/', try removing this. Also the '=' is can be replaced by a space, I believe both can work. Otherwise double check the path is accurate.

Best,
Gabriel

[gdevenyi]

I solved this problem according to your advice. But I found that the "CSF mask" still has problems.

Is this a mask we supply, or did you get it from somewhere else.

Please open an issue fully describing your issue with the mask specifically separate from this discussion.

[Rachelyolo]

Thank you for your reply. After checking with the CSF mask, I have solved this problem. However, when I tried to preprocess multiple datasets, the process encountered an error after successfully processing 3 of the datasets. The error message in the log file showed that "Workflow did not execute cleanly. Check log for details".

Could you help me with this? Thank you very much!

[Gab-D-G]

Hi, the error will be found in the log file, you should be able to the specific problem if you search for 'error'. Please share the log file for us to help.

Gabriel

[Rachelyolo]

Here is the log file. rabies_preprocess.log
Thank you very much!

Best,
Qiuyi

[Gab-D-G]

You are getting <Signals.SIGBUS: 7> errors at various pipeline stages, e.g.:

    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'antsMotionCorrStats -m /preprocess/main_wf/bold_main_wf/bold_hmc_wf/_scan_info_subject_idLPS.session3_split_name_sub-LPS_ses-3_T2w/_run_2/ants_MC/ants_mc_tmp/motcorrMOCOparams.csv -o motcorr_vol19.mat -t 19' died with <Signals.SIGBUS: 7>.

Other users have encountered this issue #349 , but this is not a RABIES error, rather it has something to do with your computing platform. You may want to review resource allocation when running the pipeline. You could attempt running the pipeline with -p Linear and see if that mitigates the issue (although it will be slower to run).