Hi
I want to process the diffusion data from the HCP-development dataset with the already preprocessed structural data. However, I failed trying to import the processed data with the import_hcp
command and the new --processed_data
flag (QuNex v0.99.2).
Do I miss some naming specifications or extra settings?
Many thanks in advance! <3
My command is:
qunex_container import_hcp --sessionsfolder=$STUDYDIR/sessions \
--inbox=$RAWDIR/imagingcollection01 --action='copy' \
--overwrite=yes --archive='leave' \
--processed_data=$RAWDIR/fmriresults01
And runs with the following log:
# Generated by QuNex 0.99.2 on 2024-02-01_17.44.49.906323
#
call: gmri import_hcp sessionsfolder="/fast/scratch/users/martinl_c/dHCP_diffusion/sessions" inbox="/fast/scratch/users/martinl_c/raw_data/imagingcollection01" action="copy" overwrite="yes" archive="leave" processed_data="/fast/scratch/users/martinl_c/raw_data/fmriresults01"
-----------------------------------------
Running import_hcp
==================
--> identifying files in /fast/scratch/users/martinl_c/raw_data/imagingcollection01
--> mapping files to QuNex hcpls folders
ERROR: Could not parse file: /fast/scratch/users/martinl_c/raw_data/imagingcollection01/manifests/HCD0001305_V1_MR_UnprocTfmriCarit_manifest.json
ERROR: Could not parse file: /fast/scratch/users/martinl_c/raw_data/imagingcollection01/manifests/HCD0001305_V1_MR_UnprocRfmri_manifest.json
ERROR: Could not parse file: /fast/scratch/users/martinl_c/raw_data/imagingcollection01/manifests/HCD0001305_V1_MR_UnprocPcasl_manifest.json
ERROR: Could not parse file: /fast/scratch/users/martinl_c/raw_data/imagingcollection01/manifests/HCD0001305_V1_MR_UnprocTfmriGuessing_manifest.json
--> hcpls for session HCD0001305_V1_MR already exists: cleaning session
info: subject HCD0001305, session V1_MR
Running map_hcpls2nii for subject HCD0001305, session V1_MR
===========================================================
--> filesort: name_type_se
--> cleaned nii folder, removed existing files
--> removed existing session.txt file
--> removed existing session_hcp.txt file
--> linked 01.nii.gz <-- HCD0001305_V1_MR_T1w_MPR_vNav_4e_e1e2_mean.nii.gz
--> linked 02.nii.gz <-- HCD0001305_V1_MR_T2w_SPC_vNav.nii.gz
--> linked 03.nii.gz <-- HCD0001305_V1_MR_tfMRI_CARIT_AP.nii.gz
--> linked 04.nii.gz <-- HCD0001305_V1_MR_tfMRI_CARIT_PA.nii.gz
--> linked 05.nii.gz <-- HCD0001305_V1_MR_dMRI_dir98_AP.nii.gz
==> WARNING: bval/bvec files were not found and were not mapped for 05.nii.gz!
==> ERROR: bval/bvec files were not found and were not mapped: 05.bval/.bvec <-- HCD0001305_V1_MR_dMRI_dir98_AP.bval/.bvec
--> linked 06.nii.gz <-- HCD0001305_V1_MR_dMRI_dir98_PA.nii.gz
==> WARNING: bval/bvec files were not found and were not mapped for 06.nii.gz!
==> ERROR: bval/bvec files were not found and were not mapped: 06.bval/.bvec <-- HCD0001305_V1_MR_dMRI_dir98_PA.bval/.bvec
--> linked 07.nii.gz <-- HCD0001305_V1_MR_dMRI_dir99_AP.nii.gz
==> WARNING: bval/bvec files were not found and were not mapped for 07.nii.gz!
==> ERROR: bval/bvec files were not found and were not mapped: 07.bval/.bvec <-- HCD0001305_V1_MR_dMRI_dir99_AP.bval/.bvec
--> linked 08.nii.gz <-- HCD0001305_V1_MR_dMRI_dir99_PA_SBRef.nii.gz
--> linked 09.nii.gz <-- HCD0001305_V1_MR_dMRI_dir99_PA.nii.gz
--> linked 10.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap1_AP.nii.gz
--> linked 11.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap1_PA.nii.gz
--> linked 12.nii.gz <-- HCD0001305_V1_MR_rfMRI_REST1_AP_SBRef.nii.gz
--> linked 13.nii.gz <-- HCD0001305_V1_MR_rfMRI_REST1_AP.nii.gz
--> linked 14.nii.gz <-- HCD0001305_V1_MR_rfMRI_REST1_PA.nii.gz
--> linked 15.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap2_AP.nii.gz
--> linked 16.nii.gz <-- HCD0001305_V1_MR_tfMRI_EMOTION_PA_SBRef.nii.gz
--> linked 17.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap2_PA.nii.gz
--> linked 18.nii.gz <-- HCD0001305_V1_MR_tfMRI_GUESSING_AP_SBRef.nii.gz
--> linked 19.nii.gz <-- HCD0001305_V1_MR_tfMRI_GUESSING_AP.nii.gz
--> linked 20.nii.gz <-- HCD0001305_V1_MR_tfMRI_GUESSING_PA.nii.gz
--> linked 21.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap3_AP.nii.gz
--> linked 22.nii.gz <-- HCD0001305_V1_MR_SpinEchoFieldMap3_PA.nii.gz
--> linked 23.nii.gz <-- HCD0001305_V1_MR_rfMRI_REST2_AP_SBRef.nii.gz
===> WARNING:
Not all actions completed successfully!
Some files for session HCD0001305_V1_MR were not mapped successfully!
Please check logs and data!
--> copying processed data
Final report
============
subject HCD0001305, session V1_MR failed
===> ERROR in completing import_hcp:
Some actions failed
Please check report!
-----------------------------------------
Finished at 2024-02-01 17:45:02