Thanks Saad for your answer.
We completed the first part and we obtained the nii.gz files with the
images of fibers but it did not make the output test file with the
probability of connecting (that is the important point). We don't
understand how to use --s2tastext option.
This is our command line:
probtrackx --mode=simple
--seedref=/usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/nodif_brain_mask
-o test1.nii.gz -x /usr/local/freesurfer/subjects/patient1/dti/coord.txt
-l -c 0.2 -S 2000 --steplength=0.5 -P 5000 --forcedir --opd -s
/usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/merged
-m
/usr/local/freesurfer/subjects/patient1/dti/DTI_BEDPOSTX.bedpostX/nodif_brain_mask
--dir=/usr/local/freesurfer/subjects/patient1/dti/test1 --s2tastext
Where did we make the mistake?
Bests
Cinzia
>Hi - if the idea is to use implant coordinates as seed points, then you
do
> not need to create volume-like masks for that, you can use probtrackx in
"simple" mode and input the coordinates as an ascii text file.
>
> For example:
>
> probtrackx -x coords.txt --mode=simple [other options]
>
> where coords.txt looks like this:
> x1 y1 z1
> x2 y2 z2
> ...
>
>
> x,y,z being *voxel* coordinates in seed space (better to use structural
space in your case i guess).
>
> If you are interested in estimating the probability of connecting to a
set
> of targets (as in seed-to-target), then you can use the --s2tastext
option. The output will be a text file that represents a matrix with
size
> (#seed coords)X(# targets).
>
>
> Cheers,
> Saad.
>
>
> On 13 Apr 2011, at 12:18, Cinzia Cecchetto wrote:
>
>> Dear FSL experts,
>> I have to process a set of DTI images of patients. These patients have
several implants in the deep brain and I want to know the fibers
between
>> these areas (I'm not interested about images of fiber but numbers,
density, length ecc), I know everything about these points.
>> I thought to use PROBTRACKX of FSL: I completed eddy current correction
and bedpostx but I have some problems to insert multiple masks. Do I
have to create a 3D images for each ROI? (there are about 100 ROI in
each patients) or are there any methods to automatically insert the
coordinates? Which is the better space (diffusion, structural or
standard space) to create seed masks? Which file format do I have to
use to write the masks?
>> Bests
>> Cinzia
>
> --
> 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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