Hi - you've discovered a hidden option in probtrackx! congratulations :)
The lrmask is used to store the result of matrix2 (e.g. Seed_to_RestOfBrain-type matrix). The number of columns in this matrix is equal to the number of voxels in seed space, which can be BIG.
In order to be able to store this amount of data, we provide the option of specifying the seed space in a lower resolution.
Note that: We do not offer support (yet) for this option, and its usage is likely to change in the very near future before it is released.
Cheers,
Saad.
On 4 Nov 2010, at 11:30, Corina Melzer wrote:
> Hi,
>
> I'm using probtrackx for tractography and I am wondering about the probtrackx option --lrmask, for which I couldn't find any documentation. I know it is for defining a low resolution mask, if seed space is in high resolution. But what is it really doing and why is it necessary?
>
> I'm asking this, since when starting tractography using our data I need to specify this low-res mask. Otherwise I'll get an error message: "Image Exception: #22 :: Failed to read volume". By the way it was hard to figure out, what the real problem behind this error was. Our seed space is 160x200x160 (1mm) and diffusion space is 182x128x72 (1.7mm).
>
> I use the following command for tractography:
> probtrackx -s <bedpost_dir>/merged -m <bedpost_dir>/nodif_brain_mask --xfm=anat2diff.mat -x fdt_coordinates.txt --seedref=./t1.brain --opd -P 5000 --loopcheck --forcedir --omatrix2 --dir=connect --s2tastext --mode=simple [--lrmask=./lrmask_5mm.nii.gz]
>
> Do you additionally have any suggestions concerning the resolution of this lrmask and how does this influence my tractograms?
>
> Thanks for your help.
> Corina
>
--
Saad Jbabdi
University of Oxford, FMRIB Centre
JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466 (fax 717)
www.fmrib.ox.ac.uk/~saad
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