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
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