...

1. Copy the FSL-compatible file to the new folder (optional, rename to something simple, if the original file name is cumbersome)
2. Within Linux, open a terminal
3. 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.

   
   
4. 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: Image Added

5. Wait several minutes; if the process is successful, you will see multiple files (see below)
6. 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).
7. Compare the location of segmented structures, which are numbered according to the "CMA Standard Labels."
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Anchor
labels 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