[RESOLVED] Hcp_pre_freesurfer Files missing PreFS can not be run

Run “qunex_container hcp_pre_freesurfer --sessionsfolder=“pathtostudy/sessions/” --sessions=“pathtostudy/processing/batch_hcp.txt” --container=”${QUNEX_CONTAINER}" --overwrite=yes --hcp_brainsize=“170”, and qunex reported
"Session id: subid
[started on Saturday, 21. August 2021 16:26:29]
Running HCP PreFreeSurfer Pipeline [HCPStyleData] …

—> ERROR: Could not find T1w image file. []
—> ERROR: The requested HCP processing mode is ‘HCPStyleData’, however, no T2w image was specified!
Consider using LegacyStyleData processing mode.
—> WARNING: No distortion correction method specified.
—> Due to missing files session can not be processed.
HCP PreFS completed on Saturday, 21. August 2021 16:26:29

===> Final report for command hcp_pre_freesurfer
… subid—> Files missing, PreFS can not be run
The dataset was imported by import_bids and batch_hcp.txt was created from create_batch.
T1w and T2w are under “pathtostudy/sessions/subid/bids” .

What might be the problems? Thanks!


Welcome to QuNex forums.

It seems like something went wrong during the data onboarding phase. Could you please provide all the qunex command calls that you made prior to hcp_pre_freesurfer, starting with create_study. Furthermore, it would also greatly help, if you could attach the batch_hcp.txt file to this forum post. The more information you can provide, the easier it is for me to investigate.

Since it has been two weeks since the last post, I will mark this as resolved. ywang, if this is still an issues please let us know and we will do our best to resolve it.