Hi Xinyang,

That alignment looks ok to me, but I'm guessing that you actually want the probability maps for each structure, rather than discrete labels - if this is the case, then you need to be looking at the JHU-ICBM-tracts-prob* files.

The maxprob images are thresholded versions of the probabilistic atlas, with the probability maps of all structures combined into a single 3D image. In voxels where the probabilities for two or more structures overlap, the voxel will be given the label for the structure with the maximum probability (hence the name maxprob).

Cheers,

Paul

On 23 July 2018 at 09:24, Xinyang Liu <[log in to unmask]> wrote:
Hi Paul. That is the thing which confuses me. 

From the fslview (please see the screenshot attached),  we can see that the structure (e.g. Cingulum L) of "JHU White-Matter Tractography atlas" from the Atlas Inspector does not overlap well with the "JHU-ICBM-tracts-maxprob-thr0-2mm", neither the "thr 25" or "thr 50". Do you know why that happens? Thanks.

Best regards,
Xinyang


At 2018-07-23 15:56:08, "paul mccarthy" <[log in to unmask]> wrote:
Hi Xinyang,

As far as I'm aware, the JHU-ICBM-tracts-maxprob* files are the files you're looking for.

Cheers,

Paul

On 23 July 2018 at 08:40, Xinyang Liu <[log in to unmask]> wrote:
Hi, Paul. Thank you very much for your reply.  I will try that.

By the way, I have an additional question about using the "JHU White-Matter Tractography atlas". I cannot find it in the FSL standard atlases folder. It seems the existed "JHU-ICBM-tracts-maxprob*" files do not match it. Do you have any suggestion  about how to find the  "JHU White-Matter Tractography atlas"? Thanks a lot.

Best,
Xinyang

At 2018-07-23 15:33:19, "paul mccarthy" <[log in to unmask]> wrote:
Hi Xinyang,

You can use FSLeyes to do this. The latest version of FSLeyes has a "bucket fill" option.


Cheers,

Paul

On 23 July 2018 at 03:59, Xinyang Liu <[log in to unmask]> wrote:
Dear FSL experts,

Hi. Could we ask for some help? We want to draw ROIs on MRI image slices like the picture attached for fibre tracking. Could you please tell us if we can do this with FSL and if so, which command should we use? Thank you very much.

Best regards,
Xinyang



 

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