FSL FLIRT only outputs mat files

Hi all,

I am working with a group of students through analyzing the Stroop data on openneuro.org. While I can use flirt from the gui in one step to coregister the functional to anatomical data for any one participant, some students only ever get the mat file. I’m having them use the command line flirt to then apply the transformation matrix file. However, there is not documentation that explains why someone would only get a transformation matrix while others get the matrix and the transformed functional data. I have a slightly older version of FSL (5.0.10), could that be a factor?



would it be possible for you to share the exact command you used?
That’d make it easier for others to help you.

Ah yes. My bad.

So the students just used the GUI (not the command line) to apply flirt. This is supposed to generate both a mat file and the transformed functional data. However they only get a mat file. I then have them use the flirt command this way:

flirt -in FUNCTIONAL -ref T1_IMAGE -applyxfm -init GUIMATRIX -out OUTPUT

I haven’t heard back on wether this works for them (it works for me, but everything works for me so I’m not sure I understand what is going on with their FSL). I don’t understand why the GUI would work appropriately for me, but not for them… Is this a RAM issue?