Dear all, and especially Saad!
I have been digging this out, and I would like to discuss how to best
do this usign both tracking directions
I think best is to use the common thresholded path in MNI space to
exctract the FA (or other) values in MNI space, right.
However, when doing as Saad proposed, I can plot the FA distribution
along he distance for every tracking direction A_B and B_A
separatedly, but how could I combine both trackign directions A_B and
B_A together?
I tried using
max(dist_binA_B) minus dist_bin_BA
in order to invert the direction of the plot for the B_A condition,
however the absolute distance between comes out random as the
max(dist_binA) does not really correpond to the absolute distance
between A and B, and doesnt make much sense.
Does anyone have any other idea? Has tried something that worked?
Thanks in advance!
Markus
2010-01-31 20:45 GMT+01:00 Saad Jbabdi <[log in to unmask]>:
>
> Hi
>
>
>> 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?
>
>
> Yes that's right. you might need to discard the last column if i remember
> 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.
>
>
> Ok I've attached two matlab functions that you can add to your path.
>
> then you can use the following code:
>
> load('fa.txt');fa=fa(4,1:end);
> load('dist.txt');dist=dist(4,1:end-1);
>
> [dist_bin,fa_avg,fa_std] = get_curve(dist,fa);
> plot(dist,fa,'.');
> errorbar(dist_bin,fa_avg,fa_std);
>
>
> Cheers,
> Saad.
>
>
>
>
>
>
>
>
--
Dr Markus Gschwind
Functional Brain Mapping Laboratory | Campus Biotech - Neuroscience
Department | phone +41.22.37.90.886
postal adress: 9 Chemin des Mines | Case postale 60 | 1211 Genève 20,
Switzerland
https://sites.google.com/site/fbmlab/
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