See FSL website for analysis details.
Preparing T1 files
FSL does not read all nifti files properly, so we convert them. There was some issue with reading rotations/shears, so these are removed with reslicing. Additionally, testing on 0.65 x 0.65 x 0.0.65 mm voxel size files also needed a conversion to int16 from float 32 data format.
Manually Running and Testing
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.
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 -o CON5015
- 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."
OLD: To set up FSL FIRST to run custom VOI:
(Paul worked with Brian from FSL for a few months trying to be able to use custom VOI's, but FIRST had a major upgrade which superceeded all the changes (which never worked properly anyway).)
- Copy the updated first program (as of October 2011) created by Brian Patenaude to the FSL application folder /usr/local/fsl/bin
- Copy the file from Windows to the LinuxShare folder
- In Linux, open a file browser and go to /usr/local/fsl/bin
- Rename the old "first" executable file "first_old"
- In Linux, copy the new file to the folder 
first
- Copy and correct the special script for running the custom VOI to the FSL application folder /usr/local/fsl/bin
- Copy the file from Windows to the LinuxShare folder
- In Linux, open a file browser and go to /usr/local/fsl/bin
- Rename the old "first" executable file "first_old"
- Copy the new file to the /usr/loca/fsl/bin folder run_first_dev
- In Linux, open a terminal and run the following commands, to remove extra carraige return characters that Windows puts in text files:
[...]$ cd /usr/local/fsl/bin
[...]$ dos2unix run_first_dev