Hello,
I have a few questions regarding import_bids of qunex.
- How does import_bids support multi-session data
I tried to import a bids validated dataset of a single subject that has two scan sessions with anatomical data in the first session, the bids folder structure is:
*–sub-001
- –ses-1
-
--anat -
--fmap -
--func - –ses-2
-
--fmap -
--func
Then I got the following output folder structure inside “sessions” folder:
- –001
- –001_1
- –001_2
- –archive
- –BIDS (empty folder)
log file (inside processing/logs/comlogs) showed:
Running import_bids
created BIDS archive folder
identifying files in /myStudy/bids_data/sessions/inbox/BIDS
Inbox type: bids_study
Paths:
BIDSInfo → /myStudy/bids_data/info/bids
BIDSInbox → /myStudy/bids_data/sessions/inbox/BIDS
BIDSArchive → /myStudy/bids_data/sessions/archive/BIDS
mapping files to QuNex bids folders
processing BIDS info folder
creating bids session 001
creating bids session 001_2
creating bids session 001_1
Running map_bids2nii for subject 001
WARNING:
** Unrecognized session!**
This folder [/myStudy/bids_data/sessions/001] does not have a valid matching BIDS session!
Please check your data!
……. (Running map_bids2nii for subject 001, session 1 and session 2 were successful)
And at the end of the log file:
===> ERROR in completing import_bids:
Some actions failed
** Please check report!**
while the log file in “processing/logs/runlogs” showed:
Generated by QuNex 0.94.14
qunex import_bids
–sessionsfolder=“/myStudy/bids_data/sessions”
–inbox=“/myStudy/bids_data/sessions/inbox/BIDS”
–action=“copy”
–overwrite=“yes”
–archive=“leave”
–fileinfo=“full”
ERROR running import_bids
However, if I change the bids folder structure to the following before running “import_bids” by moving anat folder from ses-1 up one level to directly under the subject folder as:
*–sub-001
- –anat
- –ses-1
-
--fmap -
--func - –ses-2
-
--fmap -
--func
Then the import went smoothly without any warning message or error message, and the folder [/myStudy/bids_data/sessions/001] previously reported error on was not created at all.
I wonder why import_bids worked this way.
- I wonder how to run qunex pipeline on the imported bids data, especially multiple session together (as the example here for sessions/001-1 and sessions/001-2 together, as there is only anatomical data in the first session)?
After the import, under folder “sessions":
–001-1
- –behavior*
- –bids*
- –nii*
- session.txt*
–001-2
- –behavior*
- –bids*
- –nii*
- session.txt*
there are the copied and renamed nifty files in the “nii” folder, the original bids data in the “bids” folder, and a mapping file “session.txt” to show which nifty file in the “nii” folder mapped to T1w, T2w, fieldmap, fMRI data, etc. Is there a documentation page on how to run qunex on the imported data that I can refer to?
By the way, in the “session.txt” file it mentioned there should be a folder named “hcp” as:
hcp: /myStudy/bids_data/sessions/001_1/hcp
But this “hcp” folder was not created at all during the import_bids process. Is that a concern? In the log file (inside folder “processing/logs/runlogs”, it marked importing was successful:
Generated by QuNex 0.94.14
qunex import_bids
–sessionsfolder=“/myStudy/bids_data/sessions”
–inbox=“/myStudy/bids_data/sessions/inbox/BIDS”
–action=“copy”
–overwrite=“yes”
–archive=“leave”
–fileinfo=“full”
===> Successful completion of task
- I wonder how the information in the json files of the original bids dataset are used in the qunex processing pipeline?
Many thanks.
Best,
Xuejun