Hi everyone,
We have on-boarded HCP diffusion data and pre-processed this data. We now want to onboard resting state HCP data into the same folder structure but are running into the errors with import_hcp.
The error seems to be is it wants to look for hcpls data in /share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/sessions/MR/hcpls which doesn’t exist as the correct file path is /share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/sessions/NDARAB462FH0_MR/hcpls
I have tried numerous time with changing the hcplsname. I can get it to work if I create_study and create a new folder structure, however we want it in the existing folder structure not a new one.
Does anyone know a fix for this? Or is there a different way to onboard new data into an existing set up?
Thanks so much!
Call:
qunex version 0.99.2
qunex_container import_hcp \
--bind="/imgshare:/imgshare,/share/HCP-Disease/DCAM:/share/HCP-Disease/DCAM,/share/ndadata:/share/ndadata" \
--sessionsfolder="/share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/sessions" \
--inbox="/share/HCP-Disease/DCAM/data/NDARAB462FH0" \
--sessions="${SESSIONS}" \
--action="copy" \
--overwrite="no" \
--archive="leave" \
--nameformat="(?P<subject_id>[^/]+?)/unprocessed/(?P<session_name>.*?)/(?P<data>.*)" \
--hcplsname="NDARAB462FH0_MR" \
--container="${QUNEXCONIMAGE}"
Logs:
started running import_hcp at 2024-06-24 16:43:24, track progress in /share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/processing/logs/comlogs/tmp_import_hcp_2024-06-24_16.43.24.055029.log
call: gmri import_hcp sessionsfolder="/share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/sessions" inbox="/share/HCP-Disease/DCAM/data/NDARAB462FH0" action="copy" overwrite="no" archive="leave" nameformat="(?P<subject_id>[^/]+?)/unprocessed/(?P<session_name>.*?)/(?P<data>.*)" hcplsname="NDARAB462FH0_MR" sessions="NDARAB462FH0_MR"
-----------------------------------------
Running import_hcp
==================
--> identifying files in /share/HCP-Disease/DCAM/data/NDARAB462FH0
--> mapping files to QuNex hcpls folders
--> incomplete hcpls for session MR already exists: cleaning session
info: subject MR
Running map_hcpls2nii for subject MR
====================================
===> WARNING:
No hcpls folder present!
There is no hcpls data in session folder /share/HCP-Disease/DCAM/output/NDARAB462FH0_MR/sessions/MR/hcpls
Please import HCPLS data first!
Final report
============
subject MR failed
===> ERROR in completing import_hcp:
Some actions failed
Please check report!
-----------------------------------------
Finished at 2024-06-24 16:44:04