TUTORIAL FOR PREPROCESSING	

A. task-fMRI preprocessing

Requires:
-MATLAB
-SPM
-Group-ICA

*************************************************
------------------ 1. Download ------------------
*************************************************

Download fMRI sequences from https://openneuro.org/datasets/ds004144/versions/1.0.2
Download scripts from https://zenodo.org/record/6617778#.Yp6R53ZBw2w (preprocessing.rar)


*************************************************
------------------ 2. Unzip ---------------------
*************************************************

1. Copy into bids_uz
2. Open terminal in bids_uz
3. Unzip anatomical --->  gunzip sub-xx/ses-1/anat/*.nii.gz
4. Unzip functional --->  gunzip sub-xx/ses-1/func/*.nii.gz


*************************************************
--------------- 3. Reorientation ----------------
*************************************************
To reorient T1 and task-fMRI sequences:

1. Open sequence to reorient on SPM fmri
2. Select "Display" and open the sequence to be reoriented
3. Reorient it according to anterior commisure
4. Adjust rotation (pitch, roll, yaw -0.01 scale-)
5. Write parameters of orientation (as guide for the other sequences)
6. Select "Set origin"
7. Select "Reorient"
8. Select the sequence (for functional, select all volumes -0:999-)
9. Accept and save reorientation map

* Corresponding files are:
 T1: sub-xxx/anat/sub-xxx_T1w.nii
 Task: sub-xxx/func/sub-xxx_task-rest_bold.nii


*************************************************
----------- 4. Slice Time Correction ------------
*************************************************
For the reorientated fMRI-task sequences:

1. In SPM fmri select "Slice timing"
2. Load bids/derivatives/prep/stc.mat
     Parameters specified:   
	-Number of slices: 37
	- TR:		    2
	- TA: 		    1.94594594594595 **TR-(TR/nslices)**
	- Slice order:      1x37 double **interleaved button-up**
	- Reference slice: 19
	- Filename prefix:  a
3. Specify "Data" --> "Session"
4. Unselect all files
5. Select all volumes from the sequence (1:999)
6. Run
7. Review

*************************************************
---------------- 5. Realigment ------------------
*************************************************

1. Run in matlab run_realignment_estimate_reslice_TB_190704.m 
2. Review

 Parameters: (default)
 - Estimate and write
 - quality 0.9
 - sep 4
 - fwhm 5
 - rtm 0
 - interp 4
 - wrap [0 0 0]
 - mask 1

*************************************************
------------- 8. Corregistration ----------------
*************************************************

1. Run in matlab run_coregistration_estimate_TB_190712.m
2. Review histogram and T1 ovaerlaying functional

*Open SPM to obtain histograms

 Parameters:(default)
 - Estimate
 - Cost_fun nmi
 - sep [4,2]
 - fwhm [7,7]


*************************************************
-------------- 9. Normalization -----------------
*************************************************

a) Functional

1. Run in matlab run_normalization_TB_190716.m
2. Review

 Parameters:
 - estimate & write
 - biasreg 1e-04
 - biasfxhm 60
 - affreg mni
 - reg[0,1.000000000000000e-03,0.500000000000000,0.050000000000000,0.200000000000000]
 - fwhm 0
 - samp 3
 - bb [-78,-112,-70;78,76,85]
 - vox [3,3,3]
 - interp 7
 - prefix w

b) Structural

1. Open in SPM "Normalise-write)
2. Specify:
	- Subject-> Deformation field: "y" anatomical sequence
	- Subject-> Images to write: T1
	- Voxel sizesL: [1 1 1]
3. Review

*Remeber to deselect the sequences before selecting the new one for each subject


*************************************************
---------------- 9. Smoothing -------------------
*************************************************

1. Run in matlab run_smoothing_TB.m
2. Review

Parameters:
 - fwhm [6,6,6]
 - prefix s



*************************************************
------- 10. Movement parameters plot ------------
*************************************************

1. Run in matlab create_realignment_plots.m 
2. Review


*************************************************
------------- 11. Artifact remotion -------------
*************************************************

Run the GUI for Group-ICA. For each subject select 
extraction of 100 independent components using the 
Infomax algorithm and ICASSO to ensure the stability
of components. Then visualize each component and 
do a manual selection of components to keep.


*************************************************
----------- 12. First level design --------------
*************************************************

1. Run in matlab run_firstlevels_TB_161019.m 

This script needs firstlevel_job_TB_061219.mat 

Parameters:
 - High pass filter: 192 (or 128)
 - derivatives [1,1] (time and dispersion derivatives)

* To save the plot, run one by one and save in /bids/derivatives/l1/mtrx
  with mtrx_xx.jpg as filename
* For subject 08 (#5), adjust tasklenght (line 23) to 774

*************************************************
*************************************************

B. task-fMRI preprocessing

Requires:
-CONN Toolbox

1. Upload the functional and anatomical sequences to CONN
2. After setting up, a preprocessing pipeline (it can be a predefined pipeline
from the menu or following the steps mentioned for the task-fMRI sequences)
3. Set ART thresholds to >  0.9 mm for head motion, and 5 for for global signal Z score 
4. Run denoising