output folder-qsirecon only have logs folder

[JING-797]

Hi Matt,

When i used the qsiprep,i was confused with some questions. I sincerely hope you can solve my problems if it is convenient for you.

q1,With the default options, the pipeline only implemented preprocessing, and the reconstruction results were not automatically generated, Do I need to set any specfic options according to the dMRI data (e.g. --recon-spec argument)?

q2, The qsiprep have completed preprocessing pipeline, and generated qsiprep folders, but there wa no any reconstruction results . In the output dir, there was only log folder in the qsirecon folder. It reported erros in the process.

210821-17:50:56,732 nipype.workflow INFO: [Node] Finished "qsiprep_wf.single_subject_001_wf.dwi_finalize_acq_diff_wf.ds_interactive_report". 210821-17:50:56,732 nipype.workflow INFO: [Job 108] Completed (qsiprep_wf.single_subject_001_wf.dwi_finalize_acq_diff_wf.ds_interactive_report). Sentry is attempting to send 1 pending error messages Waiting up to 2 seconds Press Ctrl-C to quit

q3,I wanna continue analysis, if i chose the" --recon-spec" option, what the output dir should be input, like this " --output_dir /where/my/reconstructed/data/goes" ,Does it refer to the "sub-XX"folder generated in the proprecessing pipeline output?

$ qsiprep-docker
--bids_dir /path/to/bids
--recon_input /output/from/qsiprep
--recon_spec gqi_scalar_export.json
--output_dir /where/my/reconstructed/data/goes
--analysis_level participant
--fs-license-file /path/to/license.txt

[smeisler]

1. Yes, for qsirecon to run , --recon-spec must be specified
2. That error doesn't actually seem to be a problem, since it comes after the last step of preprocessing (that is, creation of the interactive reports). What causes this isn't known at the moment, but is working on being addressed. 3)The output dir does not need to change for running reconstruction. That is, you can use the same one as qsiprep (e.g. /bids/derivatives/). If you want to use your previously computed results, you can specify --recon-only and --recon-input, which should point to your qsiprep output folder (e.g. /bids/derivatives/qsiprep)