Download Links Description

  1. rsfmri-raw (Volume-NIFTI): （BIDS-sourcedata-fMRI-tar） the raw resting-state fMRI data in NIFTI format
  2. rsfMRI-noregr (Volume-NIFTI): (BIDS-preprocessed-volume-fMRI-tar/noregr) the resting-state fMRI data after mininal preprocessed pipeline (no temporal denosing) in NIFTI format. Data was spatial transformed to the MBMv3 template space.
  3. rsfMRI-noregr (Surface-CIFTI) : (BIDS-preprocessed-surface-fMRI_tar/noregr) the resting-state fMRI after mininal preprocessed pipeline and mapped on to the MBMv3 surface in CIFTI format.
  4. rsfMRI-regrBMWC0(Volume-NIFTI) : (BIDS-preprocessed-volume-fMRI-tar/regrBMWC0) the resting-state fMRI after full preprocessed pipeline, including mininal-preprocessing, and de-noising by regressing out linear and quadratic trends, band-pass regressors (0.01–0.1 Hz), demeaned and derivatives of motion parameters, white matter signals, csf signals, and motion-censor regressors (any TR and the previous TR were censored if the weighted euclidean norm of six motion parameters was >0.2 mm). Data was spatial transformed to the MBMv3 template space.
  5. rsfMRI-regrBMWC0 (Surface-CIFTI): (BIDS-preprocessed-surface-fMRI_tar/regrBMWC0) The full processed data mapped to the MBMv3 surface in CIFTI format.
  6. rsfMRI-regrBMWC0 (Volume-NIFTI) and rsfMRI-regrBMWC0 (Surface-CIFTI) : As above but includes the global signal regression.
  7. rsfMRI-regr: (BIDS-fMRI-regressors.zip) Motion and noises regressor used in preprocessing
  8. dMRI-raw (Volume-NIFTI): (BIDS-sourcedata-dMRI.zip) the raw diffusion MRI data in NIFTI format
  9. Tracing data only: (Neurotracing-only.zip) the neuronal tracing data mapped onto the MBMv3 template space
  10. Tracing data with v3 templates: (Neurotracing-with-v3.zip) as above but also include the MBMv3 templates
  11. Codes only: (Codes_only/) Codes only for building functional parcellation and the deep-learning parcellation generators. fMRI preprocessing Pipine (MBMv4_preprocessing_pipeline.zip) is also included in the folder.
  12. Codes with examples: (Codes_with_examples/) As above but including the example data for testing the codes. fMRI preprocessing Pipine (MBMv4_preprocessing_pipeline.zip) is also included in the folder.
  13. Sequences: (Sequences.zip) examples of Bruker Method files for MRI data acquisition
  14. Atlas V4 only: (MBMv4-only.zip) the MBMv4 atlas includes the functional network parcellation (ICA results) and the functional cortical parcellations. All parcellations are in MBMv3 template space.
  15. Atlas V4 with V3 templates: (MBMv4-with-v3.zip) As above but including the MBMv3 templates.
Note: the BIDS-sourcedata-fMRI (raw data) has a total of 713 runs, and the BIDS-preprocessed-volume-fMRI (preprocessed data) has a total of 710 runs (which was also the data used in our V4 manuscript). The three runs had extensive head motions (>10% time points were censored) and were excluded from the precessed data. Download the Table S2 for details.

Resting-state fMRI Preprocessing Pipeline

  1. noregr represents minimal preprcessing pipeline without temporal denoising.
  2. regrBMWC0 and regrBMWCG0 represent the full preprocessing pipeline with temporal denoising: a) The B represents band-passing (0.01Hz-0.1Hz); b) The M represents demeaned motion parameters and their derivatives; c) The W represents the demeaned white matter signal; d) The C represents the demeaned csf signal; e) The G represents the global signal regression (demeaned whole brain signal); f) The 0 represents the motion-censor: any TR and the previous TR were censored (set to zeros) if the motion was >0.2 mm.

Minimal preprocessed (noregr)

Minimal preprcessing pipepline involves 1) despike (3dDespike), 2) slice-timing correction (3dTshift), 3) motion correction (3dvolreg), 4) EPI distortion correction (topup). No temporal filtering or regression was performed:

#!/bin/bash
## required AFNI and FSL to be installed, and the foreach function (included in the resource pipeline).


sub=sub-IONm01 # define the animal
ses=ses-01 # define the sessions
inputdir=${BIDS_sourcedata_fMRI}/${sub}/${ses} # define input data dir
outputdir=${BIDS_preprocessed_fMRI_after}/${sub}/${ses}; mkdir -p ${outputdir} # define output data dir
tmpdir=/tmp/${sub}/${ses}; mkdir -p ${tmpdir}

topup_datain_RL=${pipeline_dir}/connectome_acq_param_blip_per2tp_RL.txt
topup_datain_LR=${pipeline_dir}/connectome_acq_param_blip_per2tp_LR.txt
topup_config=${pipeline_dir}/b02b0_marmoset.cnf
tpattern=altplus
TR=2
numCPU=8 # define the how many CPU for parallel computing
## environment variable -- DON'T CHANGE
export OMP_NUM_THREADS=${numCPU}
export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=${numCPU}
export FSLOUTPUTTYPE=NIFTI  ## dont change the format

##  ======== copy data to tmp folder ======== 
cp ${inputdir}/func/*task-rest_run*.nii.gz ${tmpdir}
gzip -d -f ${tmpdir}/*.nii.gz

## ======== despike ======== 
foreach -${numCPU}  ${tmpdir}/*task-rest_run*.nii : 3dDespike -NEW -nomask -prefix ${tmpdir}/PRE-despike.nii IN -overwrite


## ======== tshift ======== 
foreach -${numCPU} ${tmpdir}/*-despike.nii : 3dTshift -TR ${TR}s -Fourier -tpattern ${tpattern} -prefix ${tmpdir}/PRE-tshift.nii IN -overwrite

## ======== volreg (two round) ========
3dbucket -prefix ${tmpdir}/RL-vr-base.nii ${tmpdir}/${sub}_${ses}_task-rest_run-RL-1-despike-tshift.nii"[0]" -overwrite
3dbucket -prefix ${tmpdir}/LR-vr-base.nii ${tmpdir}/${sub}_${ses}_task-rest_run-LR-1-despike-tshift.nii"[0]" -overwrite

foreach -${numCPU} ${tmpdir}/*-RL-*-tshift.nii : 3dvolreg -zpad 5 -base ${tmpdir}/RL-vr-base.nii -prefix ${tmpdir}/PRE-volreg.nii -1Dfile ${tmpdir}/PRE-volreg.1D -Fourier  -overwrite IN
foreach -${numCPU} ${tmpdir}/*-LR-*-tshift.nii : 3dvolreg -zpad 5 -base ${tmpdir}/LR-vr-base.nii -prefix ${tmpdir}/PRE-volreg.nii -1Dfile ${tmpdir}/PRE-volreg.1D -Fourier  -overwrite IN

fslmerge -t ${tmpdir}/RL-vr-base.nii  ${tmpdir}/*-RL-*-tshift-volreg.nii
fslmerge -t ${tmpdir}/LR-vr-base.nii ${tmpdir}/*-LR-*-tshift-volreg.nii

fslmaths ${tmpdir}/RL-vr-base.nii -Tmean ${tmpdir}/RL-vr-base.nii
fslmaths ${tmpdir}/LR-vr-base.nii -Tmean ${tmpdir}/LR-vr-base.nii

foreach -${numCPU} ${tmpdir}/*-RL-*-tshift.nii : 3dvolreg -zpad 5 -base ${tmpdir}/RL-vr-base.nii -prefix ${tmpdir}/PRE-volreg.nii -1Dfile ${tmpdir}/PRE-volreg.1D -Fourier  -overwrite IN
foreach -${numCPU} ${tmpdir}/*-LR-*-tshift.nii : 3dvolreg -zpad 5 -base ${tmpdir}/LR-vr-base.nii -prefix ${tmpdir}/PRE-volreg.nii -1Dfile ${tmpdir}/PRE-volreg.1D -Fourier  -overwrite IN

## ======== topup ========
cp ${inputdir}/func/${sub}_${ses}_task-rest_SEEPI-RL.nii.gz ${tmpdir}/SEEPI-RL.nii.gz
cp ${inputdir}/func/${sub}_${ses}_task-rest_SEEPI-LR.nii.gz ${tmpdir}/SEEPI-LR.nii.gz

##  preprocess SEEPI for RL
3dvolreg -zpad 5 -base ${tmpdir}/RL-vr-base.nii -prefix ${tmpdir}/SEEPI-RLLR-RL.nii -Fourier -overwrite ${tmpdir}/SEEPI-RL.nii.gz
fslmaths ${tmpdir}/SEEPI-RLLR-RL.nii -Tmean ${tmpdir}/SEEPI-RLLR-RL.nii
3dvolreg -zpad 5 -base  ${tmpdir}/SEEPI-RLLR-RL.nii  -prefix  ${tmpdir}/SEEPI-RLLR-LR.nii -Fourier -overwrite ${tmpdir}/SEEPI-LR.nii.gz
fslmaths  ${tmpdir}/SEEPI-RLLR-LR.nii  -Tmean  ${tmpdir}/SEEPI-RLLR-LR.nii 
fslmerge -t ${tmpdir}/SEEPI-RLLR.nii ${tmpdir}/SEEPI-RLLR-RL.nii ${tmpdir}/SEEPI-RLLR-LR.nii 

##  preprocess SEEPI for LR
3dvolreg -zpad 5 -base ${tmpdir}/LR-vr-base.nii -prefix ${tmpdir}/SEEPI-LRRL-LR.nii -Fourier -overwrite ${tmpdir}/SEEPI-LR.nii.gz
fslmaths ${tmpdir}/SEEPI-LRRL-LR.nii -Tmean ${tmpdir}/SEEPI-LRRL-LR.nii
3dvolreg -zpad 5 -base  ${tmpdir}/SEEPI-LRRL-LR.nii  -prefix  ${tmpdir}/SEEPI-LRRL-RL.nii -Fourier -overwrite ${tmpdir}/SEEPI-RL.nii.gz
fslmaths  ${tmpdir}/SEEPI-LRRL-RL.nii  -Tmean  ${tmpdir}/SEEPI-LRRL-RL.nii
fslmerge -t ${tmpdir}/SEEPI-LRRL.nii ${tmpdir}/SEEPI-LRRL-LR.nii ${tmpdir}/SEEPI-LRRL-RL.nii

##  topup for LR
topup --imain=${tmpdir}/SEEPI-LRRL.nii --datain=${topup_datain_LR} --config=${topup_config} --out=${tmpdir}/SEEPI-LRRL-topup-results --fout=${tmpdir}/SEEPI-LRRL-fout --iout=${tmpdir}/SEEPI-LRRL-iout 
##  topup for RL
topup --imain=${tmpdir}/SEEPI-RLLR.nii --datain=${topup_datain_RL} --config=${topup_config} --out=${tmpdir}/SEEPI-RLLR-topup-results --fout=${tmpdir}/SEEPI-RLLR-fout --iout=${tmpdir}/SEEPI-RLLR-iout

##  applytopup for LR
foreach -${numCPU} ${tmpdir}/*-RL-*-volreg.nii : applytopup --imain=IN  --datain=${topup_datain_RL} --method=jac --inindex=1 --topup=${tmpdir}/SEEPI-RLLR-topup-results --out=${outputdir}/PRE-topup.nii.gz

## applytopup for RL
foreach -${numCPU} ${tmpdir}/*-LR-*-volreg.nii : applytopup --imain=IN  --datain=${topup_datain_LR} --method=jac --inindex=1 --topup=${tmpdir}/SEEPI-LRRL-topup-results --out=${outputdir}/PRE-topup.nii.gz

rename -f 's///' ${outputdir}/*
rename -f 's/-despike-tshift-volreg-topup//' ${outputdir}/*

Fully preprocessed (regrBMWC0; regrBMWCG0)

Following the Minimal preprcessing pipepline, the data were de-noised by regressing out different noise components by 3dDeconvolve and 3dTproject. The B represents band-passing (0.01Hz-0.1Hz);

The M represents demeaned motion parameters and their derivatives;

The W represents the demeaned white matter signal;

The C represents the demeaned csf signal;

The G represents the global signal regression (demeaned whole brain signal);

The 0 represents the motion-censor: any TR and the previous TR were censored (set to zeros) if the motion was >0.2 mm.

#!/bin/bash
sub=sub-IONm01 # define the animal
ses=ses-01 # define the sessions
run=run-RL-1 #define the runs
inputdir=${BIDS_preprocessed_fMRI_before}/${sub}/${ses} # define input data dir
regressordir=${BIDS_fMRI_regressors}/${sub}/${ses} # define regressor dir
numCPU=8
    ###
    ## without global signal regression
    ###
    regr_type=regrBMWC0 
    outputdir=${BIDS-preprocessed-fMRI_after}/${sub}/${ses}; mkdir -p ${outputdir} # define output dir
    
    3dDeconvolve -input ${inputdir}/${sub}_${ses}_task-rest_${run}.nii.gz \
          -censor ${regressordir}/${sub}_${ses}_task-rest_${run}_combined-censor.1D  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_bpass.1D bandpass  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_wm-demean.1D wm  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_csf-demean.1D csf  \
          -float \
          -num_stimts 12    \
          -stim_file 1 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[0]' -stim_base 1 -stim_label 1 roll_01  \
          -stim_file 2 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[1]' -stim_base 2 -stim_label 2 pitch_01 \
          -stim_file 3 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[2]' -stim_base 3 -stim_label 3 yaw_01   \
          -stim_file 4 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[3]' -stim_base 4 -stim_label 4 dS_01    \
          -stim_file 5 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[4]' -stim_base 5 -stim_label 5 dL_01    \
          -stim_file 6 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[5]' -stim_base 6 -stim_label 6 dP_01    \
          -stim_file 7 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[0]' -stim_base 7 -stim_label 7 roll_02   \
          -stim_file 8 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[1]' -stim_base 8 -stim_label 8 pitch_02  \
          -stim_file 9 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[2]' -stim_base 9 -stim_label 9 yaw_02    \
          -stim_file 10 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[3]' -stim_base 10 -stim_label 10 dS_02  \
          -stim_file 11 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[4]' -stim_base 11 -stim_label 11 dL_02  \
          -stim_file 12 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[5]' -stim_base 12 -stim_label 12 dP_02  \
          -fout -tout -x1D ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.xmat.1D \
          -xjpeg ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}.jpg \
          -x1D_uncensored ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.nocensor.xmat.1D   \
          -fitts ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_fitts \
          -errts ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_errts   \
          -bucket ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_stats  \
          -jobs ${numCPU} -overwrite -x1D_stop
          cenmode=ZERO  
    3dTproject -polort 0 -input ${inputdir}/${sub}_${ses}_task-rest_${run}.nii.gz  -censor ${regressordir}/${sub}_${ses}_task-rest_${run}_combined-censor.1D -cenmode ${cenmode} -ort ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.nocensor.xmat.1D -prefix ${outputdir}/${sub}_${ses}_task-rest_${run}.nii.gz -overwrite
          
    
    
    ###
    ## with global signal regression
    ###
    regr_type=regrBMWCG0 
    outputdir=${BIDS-preprocessed-fMRI_after}/${sub}/${ses}; mkdir -p ${outputdir}
    
    3dDeconvolve -input ${inputdir}/${sub}_${ses}_task-rest_${run}.nii.gz \
          -censor ${regressordir}/${sub}_${ses}_task-rest_${run}_combined-censor.1D  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_bpass.1D bandpass  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_wm-demean.1D wm  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_csf-demean.1D csf  \
          -ortvec ${regressordir}/${sub}_${ses}_task-rest_${run}_brain-demean.1D brain  \
          -float \
          -num_stimts 12    \
          -stim_file 1 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[0]' -stim_base 1 -stim_label 1 roll_01  \
          -stim_file 2 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[1]' -stim_base 2 -stim_label 2 pitch_01 \
          -stim_file 3 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[2]' -stim_base 3 -stim_label 3 yaw_01   \
          -stim_file 4 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[3]' -stim_base 4 -stim_label 4 dS_01    \
          -stim_file 5 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[4]' -stim_base 5 -stim_label 5 dL_01    \
          -stim_file 6 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-demean.1D'[5]' -stim_base 6 -stim_label 6 dP_01    \
          -stim_file 7 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[0]' -stim_base 7 -stim_label 7 roll_02   \
          -stim_file 8 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[1]' -stim_base 8 -stim_label 8 pitch_02  \
          -stim_file 9 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[2]' -stim_base 9 -stim_label 9 yaw_02    \
          -stim_file 10 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[3]' -stim_base 10 -stim_label 10 dS_02  \
          -stim_file 11 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[4]' -stim_base 11 -stim_label 11 dL_02  \
          -stim_file 12 ${regressordir}/${sub}_${ses}_task-rest_${run}_motion-deriv.1D'[5]' -stim_base 12 -stim_label 12 dP_02  \
          -fout -tout -x1D ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.xmat.1D \
          -xjpeg ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}.jpg \
          -x1D_uncensored ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.nocensor.xmat.1D   \
          -fitts ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_fitts \
          -errts ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_errts   \
          -bucket ${outputdir}/tmp_${sub}_${ses}_task-rest_${run}_${regr_type}_stats  \
          -jobs ${numCPU} -overwrite -x1D_stop
          cenmode=ZERO 
    3dTproject -polort 0 -input ${inputdir}/${sub}_${ses}_task-rest_${run}.nii.gz  -censor ${regressordir}/${sub}_${ses}_task-rest_${run}_combined-censor.1D -cenmode ${cenmode} -ort ${outputdir}/${sub}_${ses}_task-rest_${run}_${regr_type}.nocensor.xmat.1D -prefix ${outputdir}/${sub}_${ses}_task-rest_${run}.nii.gz -overwrite

rsfMRI-regr (BIDS-fMRI-regressors): regression parameters explaination

  1. bpass.1D: band-pass filtering regressors (0.01Hz - 0.1 Hz)
  2. brain-demean.1D: the demeaned whole brain signals
  3. combined-censor.1D: the timepoint censors of the outlier time points and the motion censors
  4. csf-demean.1D: the demeaned csf signals
  5. despike-tshift_volreg.1D: the raw motion parameters
  6. hpass.1D: the high-pass filtering regressors (0.1 Hz -)
  7. motion-censor.1D: the motion-censor: any TR and the previous TR were censored (set to zeros) if the motion was >0.2 mm.
  8. motion-CENSORTR.txt: the censored time points
  9. motion-demean.1D: the demeaned motion parameters
  10. motion-deriv.1D: the derivatives of motion parameters
  11. outcount.1D: the outlier time points (estimated by afni)
  12. outcount-censor.1D: the censor regressor of the outlier time points
  13. wm-demean.1D: the demeaned white matter signals