Question Description
I am trying to use fmriprep to process some resting state data from HCP young adult dataset and after fmriprep finish running, i found in sub-xxx_ses-01_task-rest_space_MNI152NLin2009cAsym_boldref.nii.gz file that there seems to be some artifacts in the orbital frontal cortex and anterior cingulate gyrus. I have very small intensity value at these voxels compare to other regions. this seems to be a quite consistent problem not only in one but quite a few hcp young adult data that i processed with fmriprep.
- I am wondering if anyone has encountered the same type of artifacts in orbital frontal cortex and ACC of their hcp young adult data processed using fmriprep.
- is this a issue with the dataset itself or how i run my fmriprep ? the shell script i used to run fmriprep, the json files i used for the hcp_young adult dataset, and a printed tree of my example input bids formatted directory are pasted below. Sorry if i tagged this question wrong, I am not sure if this is suppose to be a software problem with fmriprep or a neuroscience question with HCP dataset
Relevant Screenshot
Relevant Scripts
singularity run \
--bind /path/to/my/bids_formatted_hcp_youngadult_data:/data \
--bind /path/to/my/fmriprep_output_directory:/out \
fmriprep-23.2.3.simg \
/data /out participant \
--participant-label "$SUBJECT" \
--fs-no-reconall \
--nprocs 8 \
--omp-nthreads 8
crc-job-stats
Input format
.
└── ses-01
├── anat
│ ├── sub-179346_ses-01_T1w.json
│ ├── sub-179346_ses-01_T1w.nii.gz -> /179346/unprocessed/3T/179346_3T_T1w_MPR1.nii.gz
│ ├── sub-179346_ses-01_T2w.json
│ └── sub-179346_ses-01_T2w.nii.gz -> /179346/unprocessed/3T/179346_3T_T2w_SPC1.nii.gz
├── fmap
│ ├── sub-179346_ses-01_dir-LR_epi.json
│ ├── sub-179346_ses-01_dir-LR_epi.nii.gz -> /179346/unprocessed/3T/rfMRI_REST1_LR/179346_3T_SpinEchoFieldMap_LR.nii.gz
│ ├── sub-179346_ses-01_dir-RL_epi.json
│ └── sub-179346_ses-01_dir-RL_epi.nii.gz -> /179346/unprocessed/3T/rfMRI_REST1_LR/179346_3T_SpinEchoFieldMap_RL.nii.gz
└── func
├── sub-179346_ses-01_task-rest_bold.json
├── sub-179346_ses-01_task-rest_bold.nii.gz -> /179346/unprocessed/3T/rfMRI_REST1_LR/179346_3T_rfMRI_REST1_LR.nii.gz
├── sub-179346_ses-01_task-rest_sbref.json
└── sub-179346_ses-01_task-rest_sbref.nii.gz -> /179346/unprocessed/3T/rfMRI_REST1_LR/179346_3T_rfMRI_REST1_LR_SBRef.nii.gz
JSON for bold file and sbref
{
"Manufacturer": "Siemens",
"ManufacturerModelName": "Skyra",
"EchoTime": 0.0331,
"FlipAngle": 52,
"RepetitionTime": 0.72,
"MagneticFieldStrength": 3.0,
"EffectiveEchoSpacing": 0.00058,
"PhaseEncodingDirection": "i",
"TaskName": "Rest"
}
JSON for field map LR
for RL it is the same file with phase encoding direction being i-
{
"PhaseEncodingDirection": "i",
"TotalReadoutTime": 0.05162,
"IntendedFor": "ses-01/func/sub-179346_ses-01_task-rest_bold.nii.gz"
}