Thanks again.

Ran


On Thu, May 2, 2013 at 11:25 AM, Saad Jbabdi <[log in to unmask]> wrote:
Yes that's right.

Cheers
Saad

On 2 May 2013, at 17:24, Ran Xu <[log in to unmask]> wrote:

Hi Saad, 

Thanks for your help. I will try the current version. Is the current version 5.0.2, right?

Thanks.
Ran


On Thu, May 2, 2013 at 11:11 AM, Saad Jbabdi <[log in to unmask]> wrote:
Hi Ran
I had forgotten that there was a bug in the seed-to-target mode in FSL500 and FSL501.
You need to download the current version if you want to use seed-to-target.  Sorry about that.

Cheers
Saad


 

On 2 May 2013, at 16:08, Ran Xu <[log in to unmask]> wrote:

Hi Saad,

I uploaded the data of two cases, including the original data and created "seeds_to_targets.nii.gz". Both of "seeds_to_targets.nii.gz" have the large values, one looks like a spot and one looks like occupying full of whole background. I used this command for case2, similar to the case1 except for the different seed, target  and exclusion masks.
'probtrackx2 -s %s -m %s --seed=%s --targetmasks=%s --waypoints=%s --stop=%s --dir=%s --avoid=%s --onewaycondition -S 100 -c 0.7 --os2t --opd',sname, mname, seed_name4, tar_name4,tar_name4,tar_name4,result_path4,excl_mask

Please let me know if you find something.
Thank you so much.

Ran


On Thu, May 2, 2013 at 3:16 AM, Saad Jbabdi <[log in to unmask]> wrote:
Hi Ran

No you can keep the --opd option.

I am not sure what is happening here. I will need to look at your data to see if I can replicate it.  I have sent you a link to an upload website. Please follow the instructions on that link.

Cheers
Saad


On 1 May 2013, at 17:44, Ran Xu <[log in to unmask]> wrote:

Hi Saad,

Thanks for your reply. I didn't use the --pd option, instead I used --opd option. Should I delete --opd option? I also want to see the fdt_paths.nii file. 

Thanks.
Ran





On Wed, May 1, 2013 at 11:32 AM, Saad Jbabdi <[log in to unmask]> wrote:
Hi - you are probably using the --pd option (distance correction). You need to turn that off if you want streamline counts.

Cheers
Saad

On 1 May 2013, at 17:14, Ran Xu <[log in to unmask]> wrote:

Dear FSL experts,

I used probtrackx2 with 5000 streamlines for each seed voxel to create the "seeds_to_targets.nii" file. When I loaded the "seeds_to_targets.nii" file, I found some values in it are more than 5000, even reaching a value like 4488952, it's so large. Is it right? Is there a possibility that the value also includes the number of streamlines from other seed voxels passing through this seed voxel? How could I get this voxel's real streamline number because I wanna know the total connection number.
 Another  "seeds_to_targets.nii.gz" file gave me some Nan or Inf values. Is it ok if I just ignore these numbers?

Thank you so much,
Ran

--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)













--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)













--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)













--
Saad Jbabdi
University of Oxford, FMRIB Centre

JR Hospital, Headington, OX3 9DU, UK
(+44)1865-222466  (fax 717)