I am learning on the way and I am not sure about the outputs of probtracks.
As I understand, the file fdt_paths.nii.gz is in diffusion space and seeds_to_{target}.nii.gz is in the standard space.
So if I run tractography to each ROI separately(that is, with one seed mask and one target mask), how can I get the FA along the tracts from the fdt_paths.nii.gz.
Is there any standard procedure to do this thing?
 
Thanks!
 
 
 
2011-08-09
Xiangzhen Kong
发件人： Virendra Mishra
发送时间： 2011-08-02  01:04:22
收件人： FSL
抄送：
主题： Re: [FSL] Extracting FA from fdt_paths from classification targets
Hi Saad,
Thank you for your quick reply.
Cheers,
Virendra
________________________________________
From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Saad Jbabdi [[log in to unmask]]
Sent: Monday, August 01, 2011 11:54 AM
To: [log in to unmask]
Subject: Re: [FSL] Extracting FA from fdt_paths from classification targets
Hi - yes the only way to do that is to re-run tractography to each ROI separately. Sorry..
Saad.
On 1 Aug 2011, at 17:13, Virendra R Mishra wrote:
> Hello FSL Experts,
>
> We used probtrackx to generate a connectivity distribution from 1 ROI to multiple ROIs and have fdt_paths.nii.gz and seeds_to_target_{x}.nii.gz files as output files where "x" is the target ROI. We are interested in computing the FA along the tracts from the seed mask(sm) to target ROI(tROI) 1 , sm to tROI 2 until sm to ROI x. We understand that the fdt_paths file has the summed probability in each voxel and seeds_to_target_{x} file doesnot have the path information. Please correct me if I am wrong in my interpretation. Is there a way in FSL to extract only the paths from sm to tROI 1 and use this as a mask to compute FA along this tract? or the only way left is to track again from  sm to each tROI1 which is quite demanding in time?
>
> Hoping for some insights.
>
> Thank you.
>
> Cheers,
>
> Virendra
>
--
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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