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 (note output name does not include "T1")
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; ... This can be created automatically from a folder with a list of T1 files names *_T1.nii.gz from a CSPM menu:
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."

CMA Labels

10 Left-Thalamus-Proper 40
11 Left-Caudate 30
12 Left-Putamen 40
13 Left-Pallidum 40
16 Brain-Stem /4th Ventricle 40
17 Left-Hippocampus 30
18 Left-Amygdala 50
26 Left-Accumbens-area 50
49 Right-Thalamus-Proper 40
50 Right-Caudate 30
51 Right-Putamen 40
52 Right-Pallidum 40
53 Right-Hippocampus 30
54 Right-Amygdala 50
58 Right-Accumbens-area 50

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