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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).
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- 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 -o CON5015; run_first_all -i OSA5065 -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."