Instructions for response function

[jdtournier]

@wombat1

So how do i incorporate the new encoding into the track?

You’d need to run dwi2fod again with the updated encoding, but you should be able to use the same response you estimated earlier.

@wombat1

OK another freaky thing just happend I used that

$ cat encoding.b | awk ‘{ print $1, $2, -$3, $4; }’

command

and all the values in the z vector I see on the screen when i type this are minus what is actually in the encoding file when i cross check it could this be the problem? for eg, using awk {…z value might be -3, but in real encoding file its 3. I dont know why it did this.

The whole point of that command is to invert the Z component… Note the -$3 in there. That’s the most likely problem with your current encoding file, this command is trying to fix it. See e.g. here for a intro to using awk - there’s plenty of tutorials online if you just search for them.

But just to complete these instructions, what you’d need to do is take the output and paste it into a new grad_fixed.b file. The simplest way to do this is to use I/O redirection, like so:

$ cat encoding.b | awk '{ print $1, $2, -$3, $4; }' > encoding_fixed.b

You can then try using that encoding_fixed.b file instead of your old one in dwi2fod, see whether that fixes things…

If it doesn’t work, you might need play around with that command by trying to invert other components (e.g. using -$1, $2, $3, $4 will invert the x component) or swapping then around (e.g. $2, $1, $3, $4 will swap x & y).