I. Load Data

Overview

This chapter describes the major functions in the File pull-down menu. Including:

Load fMRI

How to load time-series data like fMRI or perfusion.

Load Anatomy

How to load high resolution T1- or T2-weithed anatomical images as reference background.

Load Mask

How to use a mask, segmentation or clustering results to define the analysis regions.

Use Index

How to create and load an index file to fasten the loading data process.

1. Load fMRI: load time series data

The figure below is an example of the Load fMRI menu:

1.1 Number of Scan

The total number of scan or number of repetition or number of run.

1.2 File Format

Choose from the following formats. It will automatically set the byte size of a pixel, header size, filename format and extension name .

* some GE Signa files do not have '.mr' extension, please remember to delete it in the 'Extension' (see 1.12).

You can also specify Header Size (in byte) by your self.

If you want to load files that were created on big-endian machines (like Sun SPARC, SGI, PowerPC, etc) from little-endian machines (like Intel x86), you must check the Swap Byte check-box.

1.3 Data Type

Specify how many bits are used to store a pixel/voxel. Only 4 options are available. Most medical images save a pixel/voxel in 2 bytes.

Note: currently the float data type is converted to 32-bit integer internally. Therefore decimal point is discarded.

1.4 Image Size

Specify the X and Y matrix size here (in number of pixel). The Z size is referred as Slice Number. Arbitrary matrix size (> 4) is supported.

1.5 Slice Number

The number of slice of 2D data or the z-dimension of 3D data.

1.6 Flip H-F

Flip the image in Head-Foot direction. This is to correct for the displayed orientation of Analyze format data. Default for *.img.

1.7 Filename Format

Select the naming format of different image formats. If you already selected the correct image format, you don't need to change here.

1.8 Path

Specify the data path. You can also use the Browse button to locate the path.

1.9 Prefix

Specify the exam number of GE Signa format, or the first number of Siemens format, or the filename perfix of other formats. You can also use the Browse button to see the filename, but beware to delete the unnecessary parts of the filename, e.g., extension name, after Browse.

1.10 Series Number

Specify the series number of GE Signa format or the second number of Siemens formats.

1.11 Image Number

Specify the image number for Analyze and GE Signa formats or the third number of Siemens formats.

Increment

Specify the increment of the image number. Useful for skipping even or odd slices.

Add Zero

It will add zeros to the image number to become 3-digit format, like 001, 035.

1.12 Extension

Specify the extension name here. Don't add '.' here!

1.13 Extension Range

Specify the number range for the Ext filename format.

1.14 Skip File Check

Before loading the data, FACT will check that all the files exist, file size is correct. If not, it will show warning message about the incorrect file size and/or number of file. Skip this check using this option.

1.15 Skip Scan

Skip some scans in the beginning. Useful for image formats like MGH and Bruker. If you want to skip scans for other formats, better change the series or image number.

2. Load anatomy

3. Load mask

4. Use index