Thanks a lot Anastasia.
I had an extra volume at the end of file which was just an average of all other
volumes (automatically generated by philips scanner). Removing that extra
volume solved my problem.
Thank you again,
Ali Ezzati
________________________________________
From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
Sent: Friday, May 17, 2013 11:49 AM
To: Ali Ezzati
Cc: freesurfer@nmr.mgh.harvard.edu
Subject: RE: [Freesurfer] TRACULA outputs out of expected range
Hi Ali - The last row of your gradient table is "0 0 0". And yet, based on
the b-value table, it is supposed to correspond to a diffusion-weighted
volume with b=800. So there must have been a diffusion-encoding gradient
vector that was applied to acquire that volume, and you need to find out
what that gradient vector was and put it in that line.
Also, some of the lines in the gradient table follow the Xe-Y notation and
some don't. I don't know if this will cause a problem, it's possible that
it might depending on the platform. In any case, it's good to be
consistent to be safe.
Hope this helps,
a.y
On Mon, 6 May 2013, Ali Ezzati wrote:
> Hi Anastasia,
>
> I think I still have the previous problem of "out of range outputs". For
> example: based on literature (& your previous TRACULA-bases articles) the
> expected range of mean FA value is around 0.4-0.5, but the average FA for my
> data is 0.7-0.8. The same is true with MD, RD, AD values. Comparative
> analysis between groups is not promising too. This makes me think something
> is going wrong with my analysis/settings, although I get no error during
> processing.
>
> I can only think of settings in .dmricr or bvec file to be a source of error,
> so I have attached a sample of them for one of the subjects to this email. I
> would be grateful if you could take a look at them and let me know if they
> are as expected.
>
> There are 3 .bvec files inside the "dmri" folder:
> 1- dwi_orig.mghdti.bvecs
> 2- bvecs.norot
> 3- bvecs
> The first 2 files are the same as my input .bvec file ("bvecs.norot" is
> rotated to 3 rows instead of 3 columns).
> File 3 -"bevecs"- is different from the other 2 files.
>
>
> Thank you again for your help,
> Ali
> ________________________________________
> From: Ali Ezzati
> Sent: Friday, May 03, 2013 11:54 AM
> To: Anastasia Yendiki
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: RE: [Freesurfer] TRACULA outputs out of expected range
>
> Hi Anastasia,
>
> Thank you for your response. I think I figured out what was the problem: The
> delimiter for the 3 column .bvec file MUST be SPACE/TAB, otherwise the
> program fails to reshape it correctly. In my case the delimiter was "," and
> the program was reading only the 1st column of it.
>
> I have one more question: I know that FA values might differ from study to
> study and from MRI to MRI, but what is a reasonable range for that after
> analysis with Tracula? In your study (20011) the range was ~ 0.3-0.6. But
> for in elderly population the average is around 0.2 higher. Does it sound
> normal to you? I was not able to find any study using your method in elderly
> population for comparison.
>
> Thank you,
> Ali
> ________________________________________
> From: Anastasia Yendiki [ayend...@nmr.mgh.harvard.edu]
> Sent: Tuesday, April 30, 2013 3:11 PM
> To: Ali Ezzati
> Cc: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] TRACULA outputs out of expected range
>
> Hi Ali - This is unusual. It may have something to do with system
> settings. Can you send an example of the two versions of the bvecs files
> that have the different values?
>
> Thanks,
> a.y
>
> On Mon, 29 Apr 2013, Ali Ezzati wrote:
>
>> Hello Experts,
>> I would be grateful if you could help me with this problem:
>>
>> I was able to run all steps of TRACULA on several subjects without any error
>> message, but all the final
>> outcomes (FA,MD,RD,AD values) are out of the expected range (i.e average FA
>> values for all tracts are >1).
>>
>> I tried to identify the source of this problem... clearly FA values in
>> "dmri/dtifit_FA", which is an output
>> of "prep" step are all out of range. The only source of error that I can
>> think of is .bvecs file. My input
>> .bvecs files are in 3 columns, exactly as described in the manual.
>>
>> There are two .bvecs file in the "dmri" folder. one is
>> "dwi_orig.mghdti.bvecs" which is exactly the same as
>> my input .bvecs file and the other one's name is just "bvecs", which has
>> completely different values. Could
>> this be the source of my problem? or something else is causing this.
>>
>> Thank you,
>> Ali
>>
>>
>>
>>
>
>
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