Hi Saad, thanks for your answer.
i followed your instructions and used fslmeants with the --showall option
fslmeants -i dtifit_FA.nii.gz -o FA.txt -m cst_mask.nii.gz --showall
fslmeants -i path_dist.nii.gz -o dist.txt -m cst_mask.nii.gz --showall
and used the 4th line of each textfile for plotting. Is that right?
> You can re-bin the distances using hist and calculate mean FA in each bin.
> I can send you some code if you find it hard to do this in matlab.
That'd be great.
Thanks, Michael
On 31.01.2010, at 18:54, Saad Jbabdi wrote:
> Hi michael,
>
>
> On 30 Jan 2010, at 21:39, Michael Scheel wrote:
>
>> Hi Saad, could you explain a bit more in detail how to proceed.
>> When I run probtrackx with and without the --pd option I have the two
>> probabilistic tracking distributions - how do I get from them the
>> expected path length?
>>
>> Would it work like this?
>> fslmaths corrected_path_distribution.nii.gz -div
>> uncorrected_path_distribution.nii.gz pathlength.nii.gz
>
> Yes. because the --pd option outputs the spatial pdf times the
> expected distance.
>
>>
>>> (make sure you use waypoint and stopping mask to select the tract
>>> of interest)
>>
>>
>> Why is that so important? For testing I used a single voxel as seed
>> and this seemed to work.
>> However what are the reasons for using waypoint and stopping mask?
>
> Because the idea was to plot FA along a specific tract. One way to
> isolate a specific tract is to use waypoint/exclusion masks. If you
> don't want to plot FA beyond a target region then you can use stopping
> masks.
>
>>
>>> plot FA etc. as a function of expected distance (it will be a cloud
>>> of voxels that you could re-bin according to distance).
>>
>>
>> How would I do this? I suppose there is a simple matlab command?
>
> you can use the path distribution to create a mask of the tract, then
> fslmeants to extract FA and expected distance from that mask.
>
> In matlab:
> load('fa.txt');
> load('dist.txt');
> plot(dist,fa,'.');
>
> You can re-bin the distances using hist and calculate mean FA in each
> bin.
> I can send you some code if you find it hard to do this in matlab.
>
> Cheers,
> Saad.
>
>
>>
>> Thanks, Michael
>>
>>
>>
>> On 29.01.2010, at 13:20, Martin Kavec wrote:
>>
>>> Hi Saad,
>>>
>>> makes a lot of sense. I'll certainly give it a try, to see what it
>>> gives in
>>> reality. However, this is only applicable to the tracks, which do
>>> not branch.
>>>
>>> cheers,
>>>
>>> Martin
>>>
>>> On Friday 29 January 2010 12:10:54 Saad Jbabdi wrote:
>>>> Hi
>>>> Here is a simpler alternative:
>>>>
>>>> - run probtrackx with and without --pd to get expected path length
>>>> (make sure you use waypoint and stopping mask to select the tract of
>>>> interest)
>>>> - plot FA etc. as a function of expected distance (it will be a
>>>> cloud
>>>> of voxels that you could re-bin according to distance).
>>>>
>>>> The only thing is that when comparing different subjects, you want
>>>> to
>>>> make sure you take these measurements along the same tracts, and
>>>> avoid
>>>> noisy data points from alternative routes that are not common across
>>>> subjects, but you can solve that by looking only at the overlapping
>>>> voxels across subjects in some common space.
>>>>
>>>> Does this make sense?
>>>>
>>>> Cheers,
>>>> Saad.
>>
>
> --
> 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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