[RESOLVED] Importing hcp style data

Use Questions
1

Hello! I’m trying to import HCP example data from subject 100307 (downloaded from here: Installation and Usage Instructions · Washington-University/HCPpipelines Wiki · GitHub) using the following command

qunex_container import_hcp
–sessionsfolder=“${STUDY_FOLDER}/sessions”
–inbox=“${RAW_DATA}”
–sessions=“100307_3T”
–action=“copy”
–overwrite=“yes”
–archive=“leave”
–nameformat=“(?P<subject_id>[^/]+?)/unprocessed/(?P<session_name>.?)/(?P.)”
–hcplsname=“hcpya”
–container=“${QUNEX_CONTAINER}”

This was to replicate [RESOLVED] Import HCP-YA released data

I’ve tried to modify the paths and --nameformat in several different ways but seem to be unable to get past an “IndexError: list index out of range”.

my folder structure within $RAW_DATA/100307 looks like this:

image
image969×242 40 KB

error_import_hcp_2025-03-26_04.35.53.196506.log (1.9 KB)

Any suggestions? Thanks so much!

Dustin

2

Ok, update. When I delete the Diffusion folder, things seem to work ok.

3

Hi Dustin,

Thanks for reporting this. It is indeed a bug where diffusion import does not work in some conditions that was introduced in QuNex 1.1.0. I fixed it and it will be released with the next QuNex version. Thanks for reporting this!

The workaround is either the one you found (removing diffusion data), which is OK, if you do not need diffusion. If you need diffusion try using an older container (1.0.x).

Best, Jure

4

Awesome, thanks Jure! Removing diffusion data is ok for me at this point, so I’m unblocked - thanks so much!