Subproject Leaders: Pete Molfese & Peter Bandettini
Main Question: How does sleep restriction impact anatomical and functional brains
Each participant has multiple sessions throughout the study.
The entire code for processing data for this study. The code folder includes scripts, while the swarm directory
includes the swarm files for running those scripts on a cluster or with GNU Parallel. Data were first converted to NIFTI with convert_dicom.sh
using the associated bids_config.txt file. Next anatomical data were processed in the freesurfer longitudinal pipeline
which can be done using run_freesurfer (or swarm_freesurfer.txt) and then both swarm_longitude.txt and swarm_longitude_2.txt.
Once those are completed, the afni_proc can be performed using afni_process.sh or as a batch in swarm_afni.txt.
code/convert_dicom.sh - converts dicom files to NIFTI using dcm2bids (and dcm2niix obviously)
code/bids_config.txt - bids config for dcm2bids
code/run_freesurfer.sh - script for running freesurfer recon-all
code/afni_process.sh - afni_proc.py script for processing resting state
swarm/swarm_freesurfer.txt - swarm for initial freesurfer
swarm/swarm_longitude.txt - swarm for longitudinal pipeline part 1
swarm/swarm_longitude_2.txt - swarm for longitudinal pipeline part 2
swarm/swarm_afni.txt - swarm for running afni_proc.py on all subjects and sessions
BIDS - or my best attempt.
- Baseline
- Mid-Sleep Restriction
- End Sleep Restriction
- Acute Recovery
- Long-term Recovery
├── README.md
├── sub-X
├── ses-AcuteRecovery
│ ├── anat
│ │ ├── sub-X_ses-AcuteRecovery_T1w.json
│ │ └── sub-X_ses-AcuteRecovery_T1w.nii.gz
│ ├── fmap
│ │ ├── sub-X_ses-AcuteRecovery_echo-1_blip.json
│ │ ├── sub-X_ses-AcuteRecovery_echo-1_blip.nii.gz
│ │ ├── sub-X_ses-AcuteRecovery_echo-2_blip.json
│ │ ├── sub-X_ses-AcuteRecovery_echo-2_blip.nii.gz
│ │ ├── sub-X_ses-AcuteRecovery_echo-3_blip.json
│ │ └── sub-X_ses-AcuteRecovery_echo-3_blip.nii.gz
│ └── func
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-1_bold.json
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-1_bold.nii.gz
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-2_bold.json
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-2_bold.nii.gz
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-3_bold.json
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-01_echo-3_bold.nii.gz
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-1_bold.json
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-1_bold.nii.gz
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-2_bold.json
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-2_bold.nii.gz
│ ├── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-3_bold.json
│ └── sub-X_ses-AcuteRecovery_task-rest_run-02_echo-3_bold.nii.gz
├── ses-Baseline
│ ├── anat
│ │ ├── sub-X_ses-Baseline_T1w.json
│ │ └── sub-X_ses-Baseline_T1w.nii.gz
│ ├── fmap
│ │ ├── sub-X_ses-Baseline_echo-1_blip.json
│ │ ├── sub-X_ses-Baseline_echo-1_blip.nii.gz
│ │ ├── sub-X_ses-Baseline_echo-2_blip.json
│ │ ├── sub-X_ses-Baseline_echo-2_blip.nii.gz
│ │ ├── sub-X_ses-Baseline_echo-3_blip.json
│ │ └── sub-X_ses-Baseline_echo-3_blip.nii.gz
│ └── func
│ ├── sub-X_ses-Baseline_task-rest_echo-1_bold.json
│ ├── sub-X_ses-Baseline_task-rest_echo-1_bold.nii.gz
│ ├── sub-X_ses-Baseline_task-rest_echo-2_bold.json
│ ├── sub-X_ses-Baseline_task-rest_echo-2_bold.nii.gz
│ ├── sub-X_ses-Baseline_task-rest_echo-3_bold.json
│ └── sub-X_ses-Baseline_task-rest_echo-3_bold.nii.gz
├── ses-EndSleepRestriction
│ ├── anat
│ │ ├── sub-X_ses-EndSleepRestriction_T1w.json
│ │ └── sub-X_ses-EndSleepRestriction_T1w.nii.gz
│ ├── fmap
│ │ ├── sub-X_ses-EndSleepRestriction_echo-1_blip.json
│ │ ├── sub-X_ses-EndSleepRestriction_echo-1_blip.nii.gz
│ │ ├── sub-X_ses-EndSleepRestriction_echo-2_blip.json
│ │ ├── sub-X_ses-EndSleepRestriction_echo-2_blip.nii.gz
│ │ ├── sub-X_ses-EndSleepRestriction_echo-3_blip.json
│ │ └── sub-X_ses-EndSleepRestriction_echo-3_blip.nii.gz
│ └── func
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-1_bold.json
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-1_bold.nii.gz
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-2_bold.json
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-2_bold.nii.gz
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-3_bold.json
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-01_echo-3_bold.nii.gz
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-1_bold.json
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-1_bold.nii.gz
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-2_bold.json
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-2_bold.nii.gz
│ ├── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-3_bold.json
│ └── sub-X_ses-EndSleepRestriction_task-rest_run-02_echo-3_bold.nii.gz
├── ses-LongtermRecovery
│ ├── anat
│ │ ├── sub-X_ses-LongtermRecovery_T1w.json
│ │ └── sub-X_ses-LongtermRecovery_T1w.nii.gz
│ ├── fmap
│ │ ├── sub-X_ses-LongtermRecovery_echo-1_blip.json
│ │ ├── sub-X_ses-LongtermRecovery_echo-1_blip.nii.gz
│ │ ├── sub-X_ses-LongtermRecovery_echo-2_blip.json
│ │ ├── sub-X_ses-LongtermRecovery_echo-2_blip.nii.gz
│ │ ├── sub-X_ses-LongtermRecovery_echo-3_blip.json
│ │ └── sub-X_ses-LongtermRecovery_echo-3_blip.nii.gz
│ └── func
│ ├── sub-X_ses-LongtermRecovery_task-rest_echo-1_bold.json
│ ├── sub-X_ses-LongtermRecovery_task-rest_echo-1_bold.nii.gz
│ ├── sub-X_ses-LongtermRecovery_task-rest_echo-2_bold.json
│ ├── sub-X_ses-LongtermRecovery_task-rest_echo-2_bold.nii.gz
│ ├── sub-X_ses-LongtermRecovery_task-rest_echo-3_bold.json
│ └── sub-X_ses-LongtermRecovery_task-rest_echo-3_bold.nii.gz
└── ses-MidSleepRestriction
├── anat
│ ├── sub-X_ses-MidSleepRestriction_T1w.json
│ └── sub-X_ses-MidSleepRestriction_T1w.nii.gz
├── fmap
│ ├── sub-X_ses-MidSleepRestriction_echo-1_blip.json
│ ├── sub-X_ses-MidSleepRestriction_echo-1_blip.nii.gz
│ ├── sub-X_ses-MidSleepRestriction_echo-2_blip.json
│ ├── sub-X_ses-MidSleepRestriction_echo-2_blip.nii.gz
│ ├── sub-X_ses-MidSleepRestriction_echo-3_blip.json
│ └── sub-X_ses-MidSleepRestriction_echo-3_blip.nii.gz
└── func
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-1_bold.json
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-1_bold.nii.gz
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-2_bold.json
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-2_bold.nii.gz
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-3_bold.json
├── sub-X_ses-MidSleepRestriction_task-rest_run-01_echo-3_bold.nii.gz
├── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-1_bold.json
├── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-1_bold.nii.gz
├── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-2_bold.json
├── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-2_bold.nii.gz
├── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-3_bold.json
└── sub-X_ses-MidSleepRestriction_task-rest_run-02_echo-3_bold.nii.gz
(OPTIONAL)
│ ├── EEG-MRI
│ ├── Subject X - Baseline.eeg
│ ├── Subject X - Baseline.vhdr
│ ├── Subject X - Baseline.vmrk
│ ├── Subject X - Long-Term Recovery.eeg
│ ├── Subject X - Long-Term Recovery.vhdr
│ ├── Subject X - Long-Term Recovery.vmrk
│ ├── Subject X - Long-Term Recovery.eeg
│ ├── Subject X - Long-Term Recovery.vhdr
│ ├── Subject X - Long-Term Recovery.vmrk
│ ├── Subject X - Mid-SR.eeg
│ ├── Subject X - Mid-SR.vhdr
│ ├── Subject X - Mid-SR.vmrk
│ ├── Subject X - Acute Recovery.eeg
│ ├── Subject X - Acute Recovery.vhdr
│ └── Subject X - Acute Recovery.vmrk