This page describes how to run a single subject manually, and to check the segmentation of that subject.
Under CSPM => T1, go to "T1 to FSL-Compatible", and select the T1. This will create a new file in a zipped (*.nii.gz) format, which you can open with mricron.
Name the file with "_T1" in the suffix, in order for the FSL/FIRST filters to work in later stages. E.g., CON101_T1.nii.gz.
Copy this file to the Linux system (e.g., LinuxShare).
Note that FIRST expects all files to be in the same folder, so the T1's and segmentations for all subjects will be in one location. This can make for thousands of files in that folder, but that is normal.
To test FIRST on one subject:
- Create an empty folder (e.g., LinuxShare\temp)
If you are running within Linux and don't need Windows, then create a folder (termed "directory" in Linux) wherever you want.
- Copy the FSL-compatible file to the new folder (optional, rename to something simple, if the original file name is cumbersome)
- Within Linux, open a terminal
- Move the current directory to the empty folder, e.g.: [user@localhost temp]$ cd /mnt/hgfs/LinuxShare/temp
The command "pwd" will tell you the current directory.
- Run FIRST on that file, e.g.:, [user@localhost temp]$ run_first_all -i CON5015_T1 -o CON5015
To run more than one subject at a time, enter multiple commands separated by semi colons: [.]$ run_first_all -i CON5015_T1 -o CON5015; run_first_all -i OSA5065_T1 -o OSA5065; ...
- Wait several minutes; if the process is successful, you will see multiple files (see below)
- Open the T1 (CON5015.nii.gz in the example below) in mricron, open the segmentations (CON5015_all_fast_firstseg.nii.gz below), and check segmentations ("Yoke" mricron instances).
- Compare the location of segmented structures, which are numbered according to the "CMA Standard Labels."
