Hi,
--onewaycondition and --savepaths are not documented in probtrackx2, right?
Cheers,
Andreas
probtrackx2
Part of FSL (build 4110)
probtrackx
Usage:
probtrackx -s <basename> -m <maskname> -x <seedfile> -o <output>
--targetmasks=<textfile>
probtrackx --help
Compulsory arguments (You MUST set one or more of):
-s,--samples Basename for samples files - e.g. 'merged'
-m,--mask Bet binary mask file in diffusion space
-x,--seed Seed volume or list (ascii text file) of volumes and/or surfaces
Optional arguments (You may optionally specify one or more of):
-V,--verbose Verbose level, [0-2]
-h,--help Display this message
-o,--out Output file (default='fdt_paths')
--dir Directory to put the final volumes in - code makes this directory
- default='logdir'
--forcedir Use the actual directory name given - i.e. don't add + to make
a new directory
--simple Track from a list of voxels (seed must be a ASCII list of
coordinates)
--network Activate network mode - only keep paths going through at least
one of the other seed masks
--opd Output path distribution
--pd Correct path distribution for the length of the pathways
--fopd Other mask for binning tract distribution
--os2t Output seeds to targets
--s2tastext Output seed-to-target counts as a text file (default in
simple mode)
--targetmasks File containing a list of target masks - for
seeds_to_targets classification
--waypoints Waypoint mask or ascii list of waypoint masks - only keep
paths going through ALL the masks
--waycond Waypoint condition. Either 'AND' (default) or 'OR'
--wayorder Reject streamlines that do not hit waypoints in given order.
Only valid if waycond=AND
--avoid Reject pathways passing through locations given by this mask
--stop Stop tracking at locations given by this mask file
--omatrix1 Output matrix1 - SeedToSeed Connectivity
--distthresh1 Discards samples (in matrix1) shorter than this threshold
(in mm - default=0)
--omatrix2 Output matrix2 - SeedToLowResMask
--target2 Low resolution binary brain mask for storing connectivity
distribution in matrix2 mode
--omatrix3 Output matrix3 (NxN connectivity matrix)
--target3 Mask used for NxN connectivity matrix (or Nxn if lrtarget3 is
set)
--lrtarget3 Low resolution mask used for Nxn connectivity matrix
--distthresh3 Discards samples (in matrix3) shorter than this threshold
(in mm - default=0)
--xfm Transform taking seed space to DTI space (either FLIRT matrix or
FNIRT warpfield) - default is identity
--invxfm Transform taking DTI space to seed space (compulsory when using
a warpfield for seeds_to_dti)
--seedref Reference vol to define seed space in simple mode - diffusion
space assumed if absent
--meshspace Mesh reference space - either 'freesurfer' (default) or
'caret' or 'first'
-P,--nsamples Number of samples - default=5000
-S,--nsteps Number of steps per sample - default=2000
--steplength Steplength in mm - default=0.5
--distthresh Discards samples shorter than this threshold (in mm -
default=0)
-c,--cthr Curvature threshold - default=0.2
--fibthresh Volume fraction before subsidary fibre orientations are
considered - default=0.01
-l,--loopcheck Perform loopchecks on paths - slower, but allows lower
curvature threshold
-f,--usef Use anisotropy to constrain tracking
--modeuler Use modified euler streamlining
--sampvox Sample random points within seed voxels
--randfib Default 0. Set to 1 to randomly sample initial fibres (with f >
fibthresh).
Set to 2 to sample in proportion fibres (with
f>fibthresh) to f.
Set to 3 to sample ALL populations at random (even
if f<fibthresh)
--fibst Force a starting fibre for tracking - default=1, i.e. first
fibre orientation. Only works if randfib==0
--rseed Random seed
Am 17.02.12 10:43 schrieb "Saad Jbabdi" unter <[log in to unmask]>:
>Hi Romain
>
>No the waypoint criterion in probtrackx is applied to each half
>trajectory separately. So when tracking from A, if only one half reaches
>B, then only one half is retained.
>
>One way to understand what might be happening is to use probtrackx2
>(pre-released on this list - please use it!!!).
>
>Probtrackx2 has a couple of features that can be useful for you:
> - You can chose your waypoints so that they are traversed in succession,
>in the same order as in the ascii list (--wayorder)
> - You can save your retained samples in ascii format (--savepaths) so
>that you can load them in matlab and see what's going on
> - You can chose to either retain both sides of the streamline or only
>one side (--onewaycondition) [note the default here is opposite to
>probtrackx]
> - You can have OR / AND conditions on your waypoints
>
>Cheers
>Saad.
>
>
>On 17 Feb 2012, at 09:33, romain valabregue wrote:
>
>> Hello
>>
>> We have a the same problem : we want the part of the track that only
>>goes between 2 region A and B
>> So if we choose a seed in A and a waypoint+termination in B we also get
>>fiber part that go through A in the opposite direction.
>> My understanding is that it is due to the fact that fsl track a fiber
>>in 2 direction and consider it as the same fiber
>> So starting from A in one direction it comes to B and stop but in the
>>other direction it goes where it wants
>> Is that right ?
>>
>> The solution to add an extra exclusion mask in the opposite direction
>>is not very easy and can not be 100% efficacy ...
>>
>> An easier solution would be to construct a fiber in only one direction.
>>Then we will easily get rid of the fiber part that goes in the opposite
>>direction since the opposite part will never enter in B.
>> Is there a way to restrict fsl fiber tracking in only one direction ?
>>
>> Thanks for your help (and for this nice software).
>>
>> Romain
>>
>>
>> Le 27/12/2011 13:58, Saad Jbabdi a écrit :
>>> Hi Volker
>>> If you are using B as termination, you should not see streamlines
>>>running out of B. It is more likely that these streamlines go past B
>>>without intersecting it, then come back to terminate in B.
>>> An easy way around this is to have an exclusion mask past B. In your
>>>case, track from prefrontal, terminate+waypoint at Amygdala, and add an
>>>exclusion mask e.g. a single plane caudal to the Amygdala.
>>>
>>> Cheers,
>>> Saad
>>>
>>>
>>>
>>> On 22 Dec 2011, at 13:20, Volker Baur wrote:
>>>
>>>> Dear FSL experts,
>>>>
>>>> we are running probtrackx to do tractography between two ROIs A and
>>>>B. We are only interested in the direct connection between A and B, so
>>>>tried to use A as seed and B as termination mask. The problem is that
>>>>there are still fibers running out of B into the opposite direction of
>>>>A. Also we tried to use A as seed and B as waypoint AND termination
>>>>mask. Has anyone an idea of which would be the best way to obtain only
>>>>those fibers that are exactly between the two ROIs? For example, if we
>>>>want to map tracts between a prefrontal ROI and amygdala, we are not
>>>>interested in fibers running out of the amygdala to the occipital
>>>>cortex.
>>>>
>>>> Also, is there a rationale of which of the two ROIs using as seed and
>>>>which as termination mask?
>>>>
>>>> Thanks very much for any help,
>>>> Volker
>>>>
>>> --
>>> Saad Jbabdi
>>> University of Oxford, FMRIB Centre
>>>
>>> JR Hospital, Headington, OX3 9DU, UK
>>> (+44)1865-222466 (fax 717)
>>> www.fmrib.ox.ac.uk/~saad
>>>
>>
>>
>>
>
>--
>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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