Dear QuNex Experts:
Apologies for my ignorance if this question is simply too trivial. I was trying to perform BOLDPreprocessing as described in this link with the following command:
qunex create_bold_brain_masks --sessions="processing/batch.txt" --sessionsfolder="sessions" --parsessions="1" --parelements="1" --bolds="rest" --overwrite="no"
I have previously successfully performed HCP pipeline using the following script:
PATH=${HOME}/qunex:${PATH}
export STUDY_NAME="cimt"
export WORK_DIR="${HOME}/qunex"
export QUNEX_CONTAINER="${WORK_DIR}/qunexcontainer/qunex_suite-0.93.6.sif" #"gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.93.6"
#export QUNEX_CONTAINER="gitlab.qunex.yale.edu:5002/qunex/qunexcontainer:0.93.6"
export RAW_DATA="${WORK_DIR}/data"
export INPUT_BATCH_FILE="${RAW_DATA}/006_batch.txt"
export INPUT_MAPPING_FILE="${RAW_DATA}/006_mapping.txt"
export SESSIONS="001A,001B,001C,001D,002A,002B,002C,003A,003B,003C,003D,004A,004B,004C,006A,006C"
export RUNTURNKEY_TYPE="local"
export export export RUNTURNKEY_STEPS="create_session_info,setup_hcp,create_batch,hcp_pre_freesurfer,hcp_freesurfer,hcp_post_freesurfer,hcp_fmri_volume,hcp_fmri_surface,hcp_diffusion"
qunex_container run_turnkey --rawdatainput="${RAW_DATA}" --batchfile="${INPUT_BATCH_FILE}" --mappingfile="${INPUT_MAPPING_FILE}" --workingdir="${WORK_DIR}" --projectname="${STUDY_NAME}" --path="${WORK_DIR}/${STUDY_NAME}" --sessions="${SESSIONS}" --sessionids="${SESSIONS}" --sessionsfoldername="sessions" --turnkeytype="${RUNTURNKEY_TYPE}" --container="${QUNEX_CONTAINER}" --turnkeysteps="${RUNTURNKEY_STEPS}" --overwrite="yes"
My mapping file is shown below:
# HCP mapping file
# ----------------
61 => T1w
81 => T2w
SpinEchoFieldMap_AP => SE-FM-AP
SpinEchoFieldMap_PA => SE-FM-PA
rfMRI_REST_AP => bold:rest:phenc(AP)
rfMRI_REST_PA => bold:rest:phenc(PA)
SpinEchoFieldMap_AP => SE-FM-AP
SpinEchoFieldMap_PA => SE-FM-PA
dMRI_dir98_AP => DWI:dir98_AP
dMRI_dir98_PA => DWI:dir98_PA
dMRI_dir99_AP => DWI:dir99_AP
dMRI_dir99_PA => DWI:dir99_PA
For some reason, I got the following error after running qunex create_bold_brain_masks:
Creating masks for bold runs ...
Files in 'images/functional will be processed.
Masks will be saved in 'images/boldmasks..
The command will create a mask identifying actual coverage of the brain for
each of the specified BOLD files based on its first frame.
Please note: when mapping the BOLD data, the following parameter is key:
--bolds parameter defines which BOLD files are processed based on their
specification in batch.txt file. Please see documentation for formatting.
If the parameter is not specified the default value is 'all' and all BOLD
files will be processed.
........................................................
Working on BOLD images in: /home/ehui/qunex/cimt/sessions/006C/images
Resulting masks will be in: /home/ehui/qunex/cimt/sessions/006C/images/segmentation/boldmasks
Based on the settings, rest BOLD files will be processed (see --bolds).
If already present, existing masks will not be overwritten (see --overwrite).
Processing 1 BOLDs in parallel
Working on: bold1
... bold data missing, skipping bold
Looked for:/home/ehui/qunex/cimt/sessions/006C/images/functional/bold1.nii.gz
Working on: bold2
... bold data missing, skipping bold
Looked for:/home/ehui/qunex/cimt/sessions/006C/images/functional/bold2.nii.gz
Bold mask creation completed on Thursday, 21. July 2022 16:08:04
---------------------------------------------------------
===> Final report for command create_bold_brain_masks
... 001A ---> BOLDS done: 0, missing data: 2, failed: 0, processed: 0, skipped: 0
Below is the folder structure after running the qunex_container with turnkeys:
.
├── 1
│ ├── 1_nonlin_norm.wdir
│ ├── DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased
│ ├── MotionCorrection
│ ├── MotionMatrices
│ └── OneStepResampling
├── 2
│ ├── 2_nonlin_norm.wdir
│ ├── DistortionCorrectionAndEPIToT1wReg_FLIRTBBRAndFreeSurferBBRbased
│ ├── MotionCorrection
│ ├── MotionMatrices
│ └── OneStepResampling
├── Diffusion
│ ├── data
│ ├── eddy
│ ├── QC
│ ├── rawdata
│ ├── reg
│ └── topup
├── MNINonLinear
│ ├── fsaverage
│ ├── fsaverage_LR32k
│ ├── Native
│ ├── Results
│ ├── ROIs
│ ├── StructuralQC
│ └── xfms
├── T1w
│ ├── 001A
│ ├── ACPCAlignment
│ ├── BiasFieldCorrection_sqrtT1wXT2w
│ ├── BrainExtraction_FNIRTbased
│ ├── Diffusion
│ ├── fsaverage_LR32k
│ ├── Native
│ ├── Results
│ └── xfms
├── T2w
│ ├── ACPCAlignment
│ ├── BrainExtraction_FNIRTbased
│ ├── T2wToT1wDistortionCorrectAndReg
│ └── xfms
└── unprocessed
├── BOLD_1_AP
├── BOLD_2_PA
├── Diffusion
├── SpinEchoFieldMap1
├── SpinEchoFieldMap2
├── T1w
└── T2w
Any help would be greatly appreciated! Thank you very much
Best,
Ed
.