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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 float 32 data format.
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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 format, which you can open with mricron.
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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:
- Create an empty folder (e.g., LinuxShare\temp)
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