Hi,
I found a mistake on my matlab code and corrected it, so waytotoal is
the biggest number of any element.
I have some questions to ask.
actually, my seeds are AAL template-registered brain areas. (all 116 regions)
I tried multiple mask mode in probtrackXX for whole brain connectivity
(which is 116*116), but It failed to load output files.
They were too big to load, so I ran probtrackXX with 'single
mask-multiple targets' for 116 different single masks.
After that, I obtained 116 'matrix_seed_to_all_targets.niii.gz' files,
and I conbined them into one 116*116 matrix.
I summed all streamlines that connect identical seed-to-target pair
region to get each element for matrix.
and I divided each element for each waytotal number for normalization.
1. I found that the number of streamlines connecting 'seed i -> target
i region (connecting itself)' is less than waytotal. Is it okay? I
glimpsed some 'matrix_seed_to_all_Targets.nii.gz' files, and a few
voxel's streamlines that connecting itself were less than 5000 or even
0. most of diagonal elements are not 1. Is it okay? or how can I fix this?
2. You told me that l can use each row in waytotal to normalise each
seeds_to_target file, and then average across each seed. what do you
mean average across each seed?
Thanks,
YM Huh
>
> 2013/5/16 Saad Jbabdi <[log in to unmask]>:
>> Hi
>>
>> 1) Ah so your seeds are basically one voxel each! in that case you can
>> forget about (2).
>>
>> 3) Yes waytotal should be bigger than the elements of the matrix. Did you
>> perhaps use the --pd option? In which case you need to turn it off.
>>
>> Cheers
>> Saad
>>
>> On 15 May 2013, at 14:49, Youngmin Huh <[log in to unmask]> wrote:
>>
>> I used probtrackx2 with an seed and 116 targets, and repeated it for 116
>> time changing seeds.
>> Then I calculated the matrix from 116 'matrix_seeds_to_all_targets' files.
>>
>> I have a few questions.
>>
>>
>> 1. each 'martix_seeds_to_all_targes' contrains 116*1 matrix. Do you mean I
>> should divide each elements of matrix by 'watotal' generated by identical
>> seed? Is this right way to normalize?
>>
>> 2. And what do you mean 'average across each seed'?
>>
>> 3. Isn't waytotal supposed to be larger number than any of 116*1 matrix
>> element? some element have values 10 times bigger than waytotal.
>>
>> Any comment would be appreciated.
>>
>>
>>
>> YM Huh
>>
>>
>> 2013/5/15 Saad Jbabdi <[log in to unmask]>
>>>
>>> Hi
>>> How did you form the 116*116 matrix? Did you used probtrackx2 with a
>>> list of 116 seeds and 116 targets and then calculated the matrix from the
>>> seeds_to_targets output? If that is the case, then you can use each row in
>>> waytotal to normalise each seeds_to_target file, and then average across
>>> each seed?
>>>
>>> Cheers
>>> Saad
>>>
>>> On 15 May 2013, at 10:20, YM Huh <[log in to unmask]> wrote:
>>>
>>> > Hi,
>>> > I ran whole brain probtrackX with 116 seed (AAL template), and got
>>> > seed*seed matrix (116*116).
>>> > each element contains the number of streamline connecting 2 seed areas.
>>> > because every seed region has different extent, and every subject
>>> > doesn't have same seed areas, I tried to normalize them.
>>> > I loaded one seed*all target (which is 1*116) matrix, and simply divided
>>> > it by 'waytotal'.
>>> > I expected all elements to have values between 0 and 1.
>>> > but they has values between 0 and 9.
>>> > I think waytotal is the possible maximum number of streamlines which
>>> > extends from each seed.
>>> >
>>> > How can I normalize them?
>>> > Can I use waytotal? or Do I have to find maximum number of streamlines
>>> > for each seed*target matrix and use it for normalize? (and repeat it 116
>>> > times...)
>>> >
>>> > I would appreciate any comments.
>>> >
>>> >
>>> > YM Huh
>>> >
>>
>>
>>
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