Hello.
I have some questions about fdt command line usage, if you don't mind.
I want to do two-mask symmetric tracking, but I understand that this
option is no longer available as a field in the command line input. I have
tried doing this with the '--seed' and '--mask2' options, as suggested
elsewhere on the mailing list, but simply cannot find the right combination
of commands to get this to work. Could you please give an example of the
correct command line input to use these options properly?
So I have instead been creating ASCII files, each with 2 lines specifying
the locations of the two seed images I want to use. This only seems to work
when the command contains the terms '--network --mode=seedmask'. I'm not
sure whether this is doing what I want though: I want to include only fibres
passing through both masks. Do I need a different command for this?
The other thing was that I also would like the information about the number
of included paths that you get from the waypoints.txt file. This does not
appear to be generated with the current command line setup I am using. Do I
need to set some extra option to produce this? Or is that information not
available when specifying two seeds in an ascii file like this?
[Here is an example of the command I am using:
probtrackx --network --mode=seedmask -x
/work/imaging4/Structural/CBU_DTI/pCBU080311/Tractography/Native_Space_Seeds/Wakana_et_al_ROIs/SLF/Left_Temporal_SLF/Left_Temporal_SLF_masks.txt
-l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
/work/imaging4/Structural/CBU_DTI/pCBU080311/fsl_analysis.bedpostX/merged -m
/work/imaging4/Structural/CBU_DTI/pCBU080311/fsl_analysis.bedpostX/nodif_brain_mask
--dir=/work/imaging4/Structural/CBU_DTI/pCBU080311/Tractography/Native_Space_Seeds/Wakana_et_al_ROIs/SLF/Left_Temporal_SLF
Thanks,
John Griffiths
(CSLB. U.o.Cambridge)
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