Hi Matteo
Completely agree that FSL list is your best bet for ProbTrackx - but would
also point you to:
http://www.ncbi.nlm.nih.gov/pubmed/23178227
And
http://www.jneurosci.org/content/34/30/10041.full
These might be helpful in understanding what you are seeing. If the
anterior pathways are not connectingı with the posterior pathways,
perhaps thatıs not a bad thing..
Hope this helps
Derek
On 04/02/2015 23:30, "Matteo Martino" <[log in to unmask]> wrote:
>Hello!
>
>We are new users of FSL.
>
>We performed the probabilistic tractography with probtrackx after the
>bedpostx processing. We would like to perform the structural connectivity
>on the basis of the functional connectivity. First, we constructed 2
>masks. We constructed 2 ROI (sphere of 6 mm of ray around a specific
>coordinate) that we found to be hypoconnected in FC in a previous
>analysis on the same sample. We co-registrated these ROI in the
>MNI152_T1_2mm. We binarized the 2 masks. We could correctly visualize the
>2 masks in flsview. Then, we did probtrackx by using the first mask as
>seed space (using standard2diff.mat) and the second mask as termination
>mask (we did not change all the other options, which remained standard).
>We obtained the typical four files and visualized fdt_paths.nii.gz on
>flsview. Since the two regions are in the anterior cingulum and in the
>posterior cingulum, respectively, we supposed that the pathways should
>run in the cingulum bundle. However, the pathways started from the seed
>mask but did not reach the termination mask and went widespread in
>different directions.
>
>Can you help us?
>
>Thank you very much!
>
>Matteo
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