R: [Camino-users] PICo - anatomical connectivity

[Curci Marina Carmela]

Thank you for your suggestions and informations! I'm new on this kind of stuff and sometimes I don't know how to ask help..

I tried to run procstreamline process with -resamplestepsize suggested by you and I obtained the image I expected. 
Then, if the resolution of my DTI data-set is equal to the resolution of the seed file, I will not need to resample the step size: is it right?

Another question about procstreamlines command: is it possible to specify the outputfile instead of the outputroot??

Thank you for your helpfulness
Marina

________________________________________
Inizio: Philip A Cook [cookpa at mail.med.upenn.edu]
Inviato: mercoledì 2 maggio 2012 17.42
Fine: Curci Marina Carmela
Cc: camino-users at www.nitrc.org
Oggetto: Re: [Camino-users] PICo - anatomical connectivity

Hi,

The attached image is not visible to the list. For the benefit of your inboxes, attachments to this list are limited to 128 Kb. It's preferable to upload images to a shared server and mail the link; including the commands used to generate the image is also very useful.

Anyway, I looked at the image, and I think I see the problem. It looks like you tracked in 2mm space but then produced the ACM at 1mm resolution, causing the undersampling of the ACM. To avoid this, add the following to your procstreamlines call:

    -resamplestepsize 0.25

This will ensure that the distance between points on the streamline is never more than 0.25mm, which should solve the problem. You may set this to a smaller value, depending on how liberally you want to define intersection with a voxel. Smaller values will cause processing to take longer though.

In general, if you are computing PICo image in a space other than the diffusion space, it's a good idea to resample like this. I will add this to the man page.


Phil

On May 2, 2012, at 7:51 AM, Curci Marina Carmela wrote:

> Good morning!!
>
> I have a questions for camino users: I'm trying to run PICo probabilistic tractography with DTI data-set. I have chosen to produce an anatomical connectivity map because I want only one probability map deriving from my seed file.
> When I set this option in the command procstreamlines I obtain an image like the attached one.
>
> I notice a sort of 'grid' on the image because there is a certain regular alternance between voxel with high intensity and voxels whose intensity is zero.
> Is this thing right? Why is there this effect??
>
> As usual, thanks for your informations
> Marina
>
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