Processing databases with micapipe

In this section, you will find examples of how mica-pipe optional arguments where used to process a variety of databases with different acquisitions parameters. Under the tab database structure the file organization of each dataset is listed. However you’ll only find those files relevant for the pipeline, not the full structure. Further information about the datasets such as the source, and references can be found here as well.

Microstructure-Informed Connectomics (MICs)

../../_images/mics_logo.png
Reference
Royer, J., Rodriguez-Cruces, R., Tavakol, S., Lariviere, S., Herholz, P., Li, Q, Vos de Wael, R., Paquola, C., Benkarim, O., Park, B., Lowe, A. J., Margulies, D., Smallwood, J., Bernasconi, A., Bernasconi, N., Frauscher, B., Bernhardt, B. C. An Open MRI Dataset for Multiscale Neuroscience. bioRxiv 2021.08.04.454795
Source CONP Portal: MICA-MICs
doi https://doi.org/10.1101/2021.08.04.454795
sub-HC001
└── ses-01
    ├── anat
    │   ├── sub-HC001_ses-01_acq-inv1_T1map.json
    │   ├── sub-HC001_ses-01_acq-inv1_T1map.nii.gz
    │   ├── sub-HC001_ses-01_acq-mp2rage_T1map.json
    │   ├── sub-HC001_ses-01_acq-mp2rage_T1map.nii.gz
    │   ├── sub-HC001_ses-01_T1w.json
    │   └── sub-HC001_ses-01_T1w.nii.gz
    ├── dwi
    │   ├── sub-HC001_ses-01_acq-b2000-91_dir-AP_dwi.bval
    │   ├── sub-HC001_ses-01_acq-b2000-91_dir-AP_dwi.bvec
    │   ├── sub-HC001_ses-01_acq-b2000-91_dir-AP_dwi.json
    │   ├── sub-HC001_ses-01_acq-b2000-91_dir-AP_dwi.nii.gz
    │   ├── sub-HC001_ses-01_acq-b300-11_dir-AP_dwi.bval
    │   ├── sub-HC001_ses-01_acq-b300-11_dir-AP_dwi.bvec
    │   ├── sub-HC001_ses-01_acq-b300-11_dir-AP_dwi.json
    │   ├── sub-HC001_ses-01_acq-b300-11_dir-AP_dwi.nii.gz
    │   ├── sub-HC001_ses-01_acq-b700-41_dir-AP_dwi.bval
    │   ├── sub-HC001_ses-01_acq-b700-41_dir-AP_dwi.bvec
    │   ├── sub-HC001_ses-01_acq-b700-41_dir-AP_dwi.json
    │   ├── sub-HC001_ses-01_acq-b700-41_dir-AP_dwi.nii.gz
    │   ├── sub-HC001_ses-01_dir-PA_dwi.bval
    │   ├── sub-HC001_ses-01_dir-PA_dwi.bvec
    │   ├── sub-HC001_ses-01_dir-PA_dwi.json
    │   └── sub-HC001_ses-01_dir-PA_dwi.nii.gz
    └── func
        ├── sub-HC001_ses-01_task-rest_acq-AP_bold.json
        ├── sub-HC001_ses-01_task-rest_acq-AP_bold.nii.gz
        ├── sub-HC001_ses-01_task-rest_acq-APse_bold.json
        ├── sub-HC001_ses-01_task-rest_acq-APse_bold.nii.gz
        ├── sub-HC001_ses-01_task-rest_acq-PAse_bold.json
        └── sub-HC001_ses-01_task-rest_acq-PAse_bold.nii.gz

MICs and micapipe were developed practically at the same time, therefore they are fully compatible and the default arguments are enough to process it. Modalities include high-resolution anatomical (T1-weighted), microstructurally-sensitive (quantitative T1), diffusion-weighted (three shells, 140 directions in total) and resting-state functional imaging. DWI and rsfMRI include a reverse phase encoding acquisition for geometric distortion correction.

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 mica-pipe -bids rawdata -out derivatives -sub HC001 -ses 01 -all
Using the -all flag is the same as using all the processing flags!
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 mica-pipe -bids rawdata -out derivatives -sub HC001 -ses 01 \
           -proc_structural \
           -proc_freesurfer \
           -post_structural \
           -proc_dwi \
           -SC \
           -proc_rsfmri \
           -GD \
           -Morphology \
           -MPC \
           -QC_subj
proc_structural
This section was processed with the default parameters (T1w = sub-HC001_ses-01_T1w.nii.gz).
proc_freesurfer
This section was processed with the default parameters (T1w = sub-HC001_ses-01_T1w.nii.gz).
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_dwi

This section was processed with the default parameters.

DWI shells to process: acq-b2000-91_dir-AP_dwi, acq-b300-11_dir-AP_dwi and acq-b700-41_dir-AP_dwi.

Reverse phase encoding image = sub-HC001_ses-01_dir-PA_dwi.nii.gz.

SC
This section was processed with the default parameters.
proc_rsfmri

This section was processed with the default parameters. Using melodic and FIX for nuisance regression and non linear registration (SyN) to T1w-nativepro space.

Main scan = task-rest_acq-AP_bold

Main phase encoding = task-rest_acq-APse

Reverse phase encoding = task-rest_acq-PAse

MPC

This section was processed with the default parameters.

Microstructural image = acq-mp2rage_T1map

Image for registration = acq-inv1_T1map.

Epilepsy and Cognition (EpiC-UNAM)

Reference
Rodríguez-Cruces R., Bernhardt B. C., & Concha L. (2020). Multidimensional associations between cognition and connectome organization in temporal lobe epilepsy. NeuroImage, Volume 213, June 2020, 116706.
Source Unpublished
doi https://doi.org/10.1016/j.neuroimage.2020.116706
sub-00367
└── ses-01
    ├── anat
    │   ├── sub-00367_ses-01_T1w.json
    │   └── sub-00367_ses-01_T1w.nii.gz
    ├── dwi
    │   ├── sub-00367_ses-01_acq-b2000_dir-AP_dwi.bval
    │   ├── sub-00367_ses-01_acq-b2000_dir-AP_dwi.bvec
    │   ├── sub-00367_ses-01_acq-b2000_dir-AP_dwi.json
    │   ├── sub-00367_ses-01_acq-b2000_dir-AP_dwi.nii.gz
    │   ├── sub-00367_ses-01_dir-PA_dwi.bval
    │   ├── sub-00367_ses-01_dir-PA_dwi.bvec
    │   ├── sub-00367_ses-01_dir-PA_dwi.json
    │   └── sub-00367_ses-01_dir-PA_dwi.nii.gz
    └── func
        ├── sub-00367_ses-01_task-rest_bold.json
        └── sub-00367_ses-01_task-rest_bold.nii.gz

This dataset contains T1 weighted images, a DWI single shell (b=2000, 60 directions) with a reverse phase encoding acquisition (dir-PA_dwi), and a 5 minutes length resting state fMRI.

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 mica-pipe -bids rawdata -out derivatives -sub 00367 -ses 01
           -proc_structural \
           -proc_freesurfer \
             -freesurfer_dir ./freesurfer_processed_00367 \
           -post_structural \
           -proc_dwi \
           -SC \
           -proc_rsfmri \
             -mainScanStr task-rest_bold \
             -regress_WM_CSF \
             -noFIX \
           -GD \
           -Morphology \
           -QC_subj
proc_structural
This section was processed with the default parameters (T1w = sub-00367_ses-01_T1w.nii.gz).
proc_freesurfer
This section was already processed, therefore we used the flag -freesurfer_dir to copy the already processed freesurfer files inside the derivatives/freesurfer/sub-00367_ses-01 directory
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_dwi

This section was processed with the default parameters.

DWI shells to process: acq-b2000_dir-AP_dwi

Reverse phase encoding image = sub-00367_ses-01_dir-PA_dwi.nii.gz

SC
This section was processed with the default parameters.
proc_rsfmri

White matter and CSF signal was regressed from the time-series for nuisance regression, instead of Melodic/FIX. Non linear registration (SyN) was used between the rsfMRI and T1-nativepro (default). No reverse phase encoding image was used.

Main scan = task-rest_bold (default)

Cambridge Centre for Ageing and Neuroscience (Cam-CAN)

Reference
Shafto M.A., Tyler L.K., Dixon M., Taylor J.R., Rowe J.B., Cusack R., Calder A.J., Marslen-Wilson W.D., Duncan J., Dalgleish T., Henson R.N., Brayne C., Cam-CAN, & Matthews F.E. (2014). The Cambridge Centre for Ageing and Neuroscience (Cam-CAN) study protocol: a cross-sectional, lifespan, multidisciplinary examination of healthy cognitive ageing. BMC Neurology, 14 (204)
Source Cam-CAN Data repository
doi https://doi.org/10.1186/s12883-014-0204-1
sub-CC110045
└── ses-pre
    ├── anat
    │   ├── mti_MTR.nii
    │   ├── sub-CC110045_T1w.json
    │   └── sub-CC110045_T1w.nii.gz
    ├── dwi
    │   ├── sub-CC110045_dwi.bval
    │   ├── sub-CC110045_dwi.bvec
    │   ├── sub-CC110045_dwi.json
    │   └── sub-CC110045_dwi.nii.gz
    └── func
        ├── sub-CC110045_ses-pre_ses-pre_task-Rest_bold.json
        └── sub-CC110045_ses-pre_ses-pre_task-Rest_bold.nii.gz
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 mica-pipe -bids rawdata -out derivatives -sub CC110045 -ses pre \
           -proc_structural \
           -proc_freesurfer \
             -freesurfer_dir ./freesurfer_processed_CC110045 \
           -post_structural \
           -proc_dwi \
           -SC \
           -proc_rsfmri \
             -mainScanStr task-Rest_bold \
             -regress_WM_CSF \
             -noFIX \
           -GD \
           -Morphology \
           -MPC \
             -microstructural_img sub-CC110045/ses-pre/mti_MTR.nii \
           -QC_subj \
proc_structural
This section was processed with the default parameters (T1w = sub-CC110045_T1w.nii.gz).
proc_freesurfer
This section was already processed, therefore we used the flag -freesurfer_dir to copy the already processed freesurfer files inside the derivatives/freesurfer/sub-CC110045_ses-pre directory
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_dwi

This section was processed with the default parameters. No reverse phase encoding image was used.

DWI to process: sub-CC110045_dwi.nii.gz

SC
This section was processed with the default parameters.
proc_rsfmri
White matter and CSF signal was regressed from the time-series for nuisance regression, instead of Melodic/FIX. Non linear registration (SyN) was used between the rsfMRI and T1-nativepro (default). No reverse phase encoding image was used. Main scan = task-Rest_bold

SUDMEX_CONN

Reference
Angeles-Valdez, D., Rasgado-Toledo, J., Issa-Garcia, V., Balducci, T., Villicana, V., Valencia, A., Gonzalez-Olvera, J. J., Reyes-Zamorano, E., Garza-Villarreal, E. A. 2021. SUDMEX CONN: The Mexican MRI dataset of patients with cocaine use disorder. medRxiv 2021.09.03.21263048
Source Openneuro: SUDMEX_CONN: The Mexican dataset of cocaine use disorder patients.
doi https://doi.org/10.1101/2021.09.03.21263048
sub-010
├── anat
│   ├── sub-010_T1w.json
│   └── sub-010_T1w.nii.gz
├── dwi
│   ├── sub-010_dwi.bval
│   ├── sub-010_dwi.bvec
│   ├── sub-010_dwi.json
│   └── sub-010_dwi.nii.gz
├── fmap
│   ├── sub-010_dir-PA_run-01_epi.json
│   ├── sub-010_dir-PA_run-01_epi.nii.gz
│   ├── sub-010_dir-PA_run-02_epi.json
│   └── sub-010_dir-PA_run-02_epi.nii.gz
└── func
    ├── sub-010_task-rest_bold.json
    └── sub-010_task-rest_bold.nii.gz

This dataset contains T1 weighted images, a HARDI-DWI single shell (b=3000, 120 directions) with a reverse phase encoding acquisition (dir-PA_run-01_epi), and a resting state fMRI of 10 minutes with its respective reverse phase encoding acquisition (dir-PA_run-02_epi). Both phase encoding images are in the fmap directory.

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 subjectDir=ds003346/sub-010

 mica-pipe -bids ds003346 -out derivatives -sub 010 \
           -proc_structural \
           -proc_freesurfer \
             -freesurfer_dir ./freesurfer_processed_010 \
           -post_structural \
           -proc_dwi \
             -dwi_rpe ${subjectDir}/fmap/sub-110_dir-PA_run-01_epi.nii.gz \
           -SC \
           -proc_rsfmri \
             -mainScanStr task-Rest_bold \
             -fmri_rpe ${subjectDir}/fmap/sub-110_dir-PA_run-02_epi.nii.gz
             -regress_WM_CSF \
             - GSR \
             -noFIX \
           -GD \
           -Morphology \
           -QC_subj \
proc_structural
This section was processed with the default parameters (T1w = sub-010_T1w.nii.gz).
proc_freesurfer
This section was already processed, therefore we used the flag -freesurfer_dir to copy the already processed freesurfer files inside the derivatives/freesurfer/sub-010 directory
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_dwi

This section was processed with the default parameters.

DWI to process: sub-010_dwi.nii.gz

Reverse phase encoding image = fmap/sub-110_dir-PA_run-01_epi.nii.gz

SC
This section was processed with the default parameters.
proc_rsfmri

White matter and CSF signal was regressed from the time-series for nuisance regression, instead of Melodic/FIX. Non linear registration (SyN) was used between the rsfMRI and T1-nativepro (default). Global signal regression was applied.

Main scan = task-rest_bold (default)

Reverse phase encoding = map/sub-110_dir-PA_run-02_epi.nii.gz

Midnight Scan Club MSC

Reference
Gordon E. M., Laumann T. O., Gilmore A. W., Newbold D. J., Greene D. J., Berg J. J., Ortega M., Hoyt-Drazen C., Gratton C., Sun H., Hampton J. M., oalson R. S., Nguyen A. L., McDermott K. B., Shimony J. S., Snyder A. Z. Schlaggar B. L., Petersen S. E., Nelson S. M., Dosenbach N. U. (2017). Precision functional mapping of individual human brains. Neuron, 95(4), 791-807.
Source Openneuro: The Midnight Scan Club (MSC) dataset
doi https://doi.org/10.1016/j.neuron.2017.07.011
sub-MSC01
├── ses-func01
│   └── func
│       └── sub-MSC01_ses-func01_task-rest_bold.nii.gz
├── ses-func02
│   └── func
│       └── sub-MSC01_ses-func02_task-rest_bold.nii.gz
├── ses-func03
│   └── func
│   │   └── sub-MSC01_ses-func03_task-rest_bold.nii.gz
├── ses-func04
│   └── func
│       └── sub-MSC01_ses-func04_task-rest_bold.nii.gz
├── ses-func05
│   └── func
│       └── sub-MSC01_ses-func05_task-rest_bold.nii.gz
├── ses-func06
│   └── func
│       └── sub-MSC01_ses-func06_task-rest_bold.nii.gz
├── ses-func07
│   └── func
│       └── sub-MSC01_ses-func07_task-rest_bold.nii.gz
├── ses-func08
│   └── func
│       └── sub-MSC01_ses-func08_task-rest_bold.nii.gz
├── ses-func09
│   └── func
│       └── sub-MSC01_ses-func09_task-rest_bold.nii.gz
├── ses-func10
│   └── func
│       └── sub-MSC01_ses-func10_task-rest_bold.nii.gz
└── ses-struct01
    └── anat
        ├── sub-MSC01_ses-struct01_run-01_T1w.nii.gz
        ├── sub-MSC01_ses-struct01_run-02_T1w.nii.gz
        └── sub-MSC01_ses-struct01_run-01_T2w.nii.gz

This dataset contains two sessions of structural imaging, (struct01 and struct02). However we only used the first one for processing. It does not contain DWI images, thus this step was omitted. Resting state functional acquisitions were acquired in different sessions (func01 to func10), hence each session was register to the first anatomical image (struct01).

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# Pipeline for the anatomical images struct01
mica-pipe -bids ds000224/ -out derivatives/ -sub MSC01 -ses struct01 \
           -proc_structural -t1wStr run-01_T1w,run-02_T1w \
           -proc_freesurfer \
           -post_structural \
           -proc_rsfmri \
             -regAffine -noFIX -regress_WM_CSF \
             -mainScanStr task-rest_bold \
           -GD \
           -Morphology \
           -QC_subj

# Pipeline for the functional images
for N in {01..10}; do
mica-pipe -bids ds000224/ -out derivatives/ -sub MSC01 -ses func${N} \
           -proc_rsfmri \
           -mainScanStr task-rest_bold \
           -regress_WM_CSF \
           -noFIX \
           -sesAnat struct01 \
           -QC_subj \
done
proc_structural
Structural processing used the files sub-MSC01_ses-struct01_run-01_T1w.nii.gz and sub-MSC01_ses-struct01_run-01_T2w.nii.gz to generate the nativepro file
proc_freesurfer
Freesurfer used sub-MSC01_ses-struct01_run-01_T1w.nii.gz and sub-MSC01_ses-struct01_run-01_T2w.nii.gz to generate the native surfaces.
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_rsfmri

Each functional session was processed individually and registered to the anatomical session struct01. In this example we use a for loop to iterate over each session. White matter and CSF signal was regressed from the time-series for nuisance regression, instead of Melodic/FIX. Non linear registration (SyN) was used between the rsfMRI and T1-nativepro (default). No reverse phase encoding image was used.

Main scan = task-rest_bold

Auditory localization with 7T fMRI (Audiopath)

Reference
Sitek, K. R., Gulban, O. F., Calabrese, E., Johnson, G. A., Lage-Castellanos, A., Moerel, M., Ghosh S. S. & De Martino, F. (2019). Mapping the human subcortical auditory system using histology, postmortem MRI and in vivo MRI at 7T. Elife, 8, e48932. 10.7554/eLife.48932.
Source Openneuro: Auditory localization with 7T fMRI
doi https://doi.org/10.7554/eLife.48932

Audiopath

sub-S01
└── ses-SES01
    ├── anat
    │   ├── sub-S01_ses-SES01_acq-ShortInv_run-01_T1w.json
    │   ├── sub-S01_ses-SES01_acq-ShortInv_run-01_T1w.nii.gz
    │   ├── sub-S01_ses-SES01_run-01_T1w.json
    │   ├── sub-S01_ses-SES01_run-01_T1w.nii.gz
    │   ├── sub-S01_ses-SES01_run-02_T1w.json
    │   └── sub-S01_ses-SES01_run-02_T1w.nii.gz
    ├── dwi
    │   ├── sub-S01_ses-SES01_dir-AP_run-01_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-AP_run-01_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-AP_run-01_dwi.json
    │   ├── sub-S01_ses-SES01_dir-AP_run-01_dwi.nii.gz
    │   ├── sub-S01_ses-SES01_dir-AP_run-02_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-AP_run-02_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-AP_run-02_dwi.json
    │   ├── sub-S01_ses-SES01_dir-AP_run-02_dwi.nii.gz
    │   ├── sub-S01_ses-SES01_dir-AP_run-03_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-AP_run-03_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-AP_run-03_dwi.json
    │   ├── sub-S01_ses-SES01_dir-AP_run-03_dwi.nii.gz
    │   ├── sub-S01_ses-SES01_dir-PA_run-01_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-PA_run-01_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-PA_run-01_dwi.json
    │   ├── sub-S01_ses-SES01_dir-PA_run-01_dwi.nii.gz
    │   ├── sub-S01_ses-SES01_dir-PA_run-02_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-PA_run-02_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-PA_run-02_dwi.json
    │   ├── sub-S01_ses-SES01_dir-PA_run-02_dwi.nii.gz
    │   ├── sub-S01_ses-SES01_dir-PA_run-03_dwi.bval
    │   ├── sub-S01_ses-SES01_dir-PA_run-03_dwi.bvec
    │   ├── sub-S01_ses-SES01_dir-PA_run-03_dwi.json
    │   └── sub-S01_ses-SES01_dir-PA_run-03_dwi.nii.gz
    ├── fmap
    │   ├── sub-S01_ses-SES01_acq-gre_dir-AP_run-01_epi.json
    │   ├── sub-S01_ses-SES01_acq-gre_dir-AP_run-01_epi.nii.gz
    │   ├── sub-S01_ses-SES01_acq-gre_dir-PA_run-01_epi.json
    │   └── sub-S01_ses-SES01_acq-gre_dir-PA_run-01_epi.nii.gz
    └── func
        ├── sub-S01_ses-SES01_task-rest_bold.json
        └── sub-S01_ses-SES01_task-rest_bold.nii.gz

This 7T in vivo dataset contains high resolution anatomical MRI, diffusion-weighted MRI and resting state fMRI. DWI images were acquired twice with the phase encoding direction of the second acquisition reversed with respect to the first. No real quantitative image was acquired, instead we used the T1w ShortInv for the MPC even though is not ideal. Additionally, it contains rsfMRI reverse phase encoding acquisitions for geometric distortion corrections.

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 subjectDir=./ds001942/sub-S01/ses-SES01
 dwiDir=./ds001942/sub-S01/ses-SES01/dwi
 sub=sub-S02_ses-SES01

 mica-pipe -bids ds001942/ -out . -sub S01 -ses SES01 \
           -proc_structural -t1wStr run-01_T1w,run-02_T1w \
           -proc_freesurfer -hires \
           -post_structural \
           -proc_dwi \
             -dwi_main ${dwiDir}/${sub}_dir-AP_run-01_dwi.nii.gz,${dwiDir}/${sub}_dir-AP_run-02_dwi.nii.gz,${dwiDir}/${sub}_dir-AP_run-03_dwi.nii.gz \
             -dwi_rpe ${dwiDir}/${sub}_dir-PA_run-01_dwi.nii.gz,${dwiDir}/${sub}_dir-PA_run-02_dwi.nii.gz,${dwiDir}/${sub}_dir-PA_run-03_dwi.nii.gz \
             -rpe_all \
           -SC \
           -proc_rsfmri \
             -regAffine -noFIX -regress_WM_CSF \
             -mainScanStr task-rest_bold \
             -fmri_pe  ${subjectDir}/fmap/${sub}_acq-gre_dir-AP_run-01_epi.nii.gz \
             -fmri_rpe ${subjectDir}/fmap/${sub}_acq-gre_dir-PA_run-01_epi.nii.gz \
           -GD \
           -Morphology \
           -MPC \
             -microstructural_img ${subjectDir}/anat/${sub}_acq-ShortInv_run-01_T1w.nii.gz \
             -microstructural_reg ${subjectDir}/anat/${sub}_acq-ShortInv_run-01_T1w.nii.gz \
           -QC_subj
proc_structural
Structural processing used the files sub-S01_ses-SES01_run-01_T1w.nii.gz and sub-S01_ses-SES01_run-02_T1w.nii.gz to generate the nativepro file
proc_freesurfer
Freesurfer used sub-S01_ses-SES01_run-02_T1w.nii.gz to generate the native surfaces. We used the hires option as is recommended for 7T isometric acquisition with high resolution or below, in this case the voxel size is 0.3x0.3x0.3 mm3.
post_structural
This section was processed with the default parameters.
Morphology
This section was processed with the default parameters.
GD
This section was processed with the default parameters.
proc_dwi

DWI directions were acquired twice with opposite phase encoding directions, thus we used the option rpe_all for the processing.

Main DWI shells to process: dir-AP_run-01, dir-AP_run-02 and dir-AP_run-03

Reverse phase encoding DWI = dir-PA_run-01, dir-PA_run-02 and dir-PA_run-03

SC
This section was processed with the default parameters.
proc_rsfmri

White matter and CSF signal was regressed from the time-series for nuisance regression, instead of Melodic/FIX. Only affine registration between the rsfMRI and T1-nativepro was performed.

Main scan = task-rest_bold

Main phase encoding = fmap/${sub}_acq-gre_dir-AP_run-01_epi

Reverse phase encoding = fmap/${sub}_acq-gre_dir-PA_run-01_epi

MPC
The microstructural image as the image to register to freesurfer space were the same = acq-ShortInv_run-01_T1w.