[RESOLVED] Hcp_pre_freesurfer Files missing PreFS can not be run

Use Questions
1

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!

2

Hi!

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.

3

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.