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.
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The command "pwd" will tell you the current directory.
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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_devThe following pages detail step-by-step how to set up and run FIRST, and are based on the FSL website.
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