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 flaot 32 data format.
Manual Testing
Under CSPM => T1, go to "T1 to FSL-Compatible, and select the T1. This will create a new file in a zipped format, which you can open with mricron.
Copy this file to the Linux system (e.g., LinuxShare). To test FIRST:
- 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).
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