ofgulban

// Brainvoyager batch script for functional MRI data (.fmr) preprocessing.
//
// For more information, check the scripting guide:
// http://support.brainvoyager.com/automation-aamp-development/46-writing-scripts/133-scripting-reference-guide.html

var bvqx = BrainVoyagerQX;
bvqx.PrintToLog("---");

//----------------------------------------------------------------

ofgulban

// Batch script for VTC creation.
// From native functional data space to an anatomical data to ACPC and to TAL
//
// For more information, check the scripting guide:
// http://support.brainvoyager.com/automation-aamp-development/46-writing-scripts/133-scripting-reference-guide.html

var bvqx = BrainVoyagerQX;
bvqx.PrintToLog("---");

//----------------------------------------------------------------

ofgulban

"""Test GL volume tool with MRI data."""

from pyqtgraph.Qt import QtCore, QtGui
import pyqtgraph.opengl as gl
import numpy as np
from nibabel import load

# get MRI data
nii = load('/path/to/your/file/T1w.nii.gz')
data = nii.get_data()

ofgulban

"""Dilation, erosion, opening, closing operations on binary nifti files."""

import os
import numpy as np
from scipy.ndimage import morphology
from nibabel import load, save, Nifti1Image

# Load data
nii = load('/path/to/your/file.nii.gz')
basename = nii.get_filename().split(os.extsep, 1)[0]

ofgulban

"""Connected clusters cluster size thresholding commandline interface."""

import os
import argparse
import numpy as np
from nibabel import load, save, Nifti1Image
from skimage.measure import label

parser = argparse.ArgumentParser()

ofgulban

% Convert Brainvoyager VMP files to nii using neuroelf.

% Select VMR
[vmr_fileName, vmr_pathName] = uigetfile('.vmr');
vmr = xff(fullfile(vmr_pathName, vmr_fileName));

% Select VMP
[vmp_fileName, vmp_pathName] = uigetfile('.vmp');
vmp = xff(fullfile(vmp_pathName, vmp_fileName));
map_index = 1;  % change this is you have multiple maps in one vmp file

ofgulban

% Convert Brainvoyager VMR or V16 files to nii using Neuroelf (v1.1 rc2).

[fileName, pathName] = uigetfile('.v16');
vmr = xff(fullfile(pathName, fileName));
vmr.ExportNifti(fullfile(pathName, [fileName(1:end-4),'.nii']) );
disp('Done.')

ofgulban

% Delete unwanted volumes from timeseries data (Brainvoyager, FMR format).
clear all;

% Enter FMR file path and volume indices to be erased
fmr_path = '/path/to/your/file.fmr';
vol_erase = [50:60, 100:103];

% Load FMR (headers) and STC (data)
fmr = xff(fmr_path);
data = fmr.Slice.STCData(:, :, :, :);

ofgulban

% Convert nifti to fmr and change the orientations.
% This scripts requires neuroelf.
%
% NOTES
% -----
% If you are getting erro about `Dyn3DToFMR`:
%    1. Clone the recent neuroelf version from <https://github.com/neuroelf/neuroelf-matlab> (this is written on 2020/04/28).
%    2. Copy `hdr_Dyn3DToFMR.m` file from neuroelf/_todo/@xff/private/ directory and paste in into neuroelf/@xff/private/ directory.
%    3. Comment out the following line fmrc.FirstDataSourceFile = hdrs.F; because otherwise it produces an error.
%    4. Add this modified neuroelf's path to your MATLAB.

ofgulban

clear all;

srf_path ='/path/to/mesh.srf'; 
srf = xff(srf_path);
out = [srf_path(1:end-4), '_POIcut.srf'];

poi = xff('/path/ro/areas.poi');
poi_idx = 1;

% (optional) cut smp