Page Comparison

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.

Image Added

Copy this file to the Linux system (e.g., LinuxShare). To test FIRST:

1. Create an empty folder (e.g., LinuxShare\temp)
2. Copy the file there (optional, rename to something simple, if the original file name is cxumbersom)
3. Within Linux, open a terminal
4. Move the current directory to the empty folder, e.g.:  [user@localhost temp]$ cd /mnt/hgfs/LinuxShare/temp
5. Run FIRST on that file, e.g.:, [user@localhost temp]$ run_first_all -i CON5015 -o CON5015
6. Wait several minutes; if the process is successful, you will see multiple files (see below)
7. Open the T1 (CON5015.nii.gz in the example below), open the segmentations (CON5015_all_fast_firstseg.nii.gz below), and check segmentations ("Yoke" mricron instances).
   Image Added

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 Image Modifiedfirst

• 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 Image Modifiedrun_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