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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.
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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:
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