Dwiextract specific volumes

[mschira]

Hi
I was trying to extract the B0 images from a dataset using dwiextract -bzero only to be told by my computer there were no B0 images.

Now upon closer inspection, there are indeed no EXACT B0, but a couple B10s i.e. a very low B value.
Apparently 10 is above the threshold to be considered “(approximately) zero” by dwiextract.
So I have been reading through the help on dwiextract

dwiextract — MRtrix 3.0 documentation

to find how to extract specific volumes for example in my case 1, 2 and 12.
The wish to extract a specified set of volumes seems a pretty standard fair to me?
I can fire up matlab to do this, but that would require exporting to .nii copying between computers etc etc.
Cheers
Mark

[maxpietsch]

To classify b-values up to 15 as b0 and extract these: dwiextract dwi.mif -bzero -config BZeroThreshold 15 b0.mif or, more generally for any volumes of interest: mrconvert -coord 3 0,4,8:2:end vols.mif.

You might want to set the b0 threshold also for other commands that extract shells or set the threshold globally in your config file.

[mschira]

Thanks Max
Especially the tip about changing the config file looking in the documentation

I guess it must be a < not a <= operation.
So I created a ~/.mrtrix.config file and put one entry
BZeroThreshold: 11

et voila it accepts the Bval 10 as zero…
Cheers
Mark