Hi Reem,
The cal_min and cal_max values are really unimportant.
They *only* control how the image looks in a viewer (the min and
max *displayed* range). However, they have absolutely no effect
on the stored intensity values. All they do is act as the initial values
in the FSLView display range boxes.
So therefore it is completely unimportant what they are set to.
However, I would still recommend using flirt_average in general as
it produces slightly sharper images due to the sinc interpolation.
One downside of the sinc interpolation is the fact that it induces
negative values (due to ringing) near the strong edges. This is
almost certainly why the cal_min gets set to a negative value.
It really isn't important what cal_min is, but that is an indication
that there is some ringing in the output data. In general I would
say that this was fine and worth the improved sharpness in the
average, but it really is a judgement call. So have a look yourself
at the output images and go with whichever one you prefer.
All the best,
Mark
On 19 Nov 2010, at 04:27, Reem Jan wrote:
> Dear Mark/Steve or anyone who is happy to answer my FLIRT query J
>
> I am in the process of averaging 2 xT1-weighted structural scans per subject to use in an FSL-VBM analysis.
>
> I have searched through the archives and found a very helpful post on flirt_average (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0803&L=FSL&P=R24790&1=FSL&9=A&J=on&d=No+Match;Match;Matches&z=4) and hence I tried using flirt_average as follows:
>
> Flirt_average 2 input_1 input_2 output_average –dof 6
>
> I noticed (using the fslinfo command) that the output_average file had a cal_min -16 and cal_max 876. When I opened the output file in fslview, these values of -16 and 876 where what I saw in the bricon min max tool bar. I compared these values to the input images which had cal_min and cal_max values of zero, however when viewed the input images in fslview I see a min value of 0 on the Bricon toolbar and a maximum value of 423.
>
> I got slightly concerned about the output (average T1) negative cal_min value (-16), so I decided to try other averaging methods to see if I get the same sort of output. I tried the following:
>
> 1. Flirt (where the reference is input_1, the input is input_2 and the output is input_2flirted) using 6 DOF
> 2. Fslmaths input_1 –add input_2flirted –div 2 output_average
>
> The output_average from this method had a cal_min of zero and cal_max of 838
>
> I then tried another method (I think this is what flirt_average script is based on)
>
> 1. Flirt (where reference is input_1, the input is input_2 and the output is input_2flirted) using 6 DOF
> 2. fslmerge –t output_merged input_1 input_2flirted
> 3. fslmaths output_merged –Tmean output_average
>
> The output_average from this method was exactly the same as the method above (cal_min of zero and cal_max of 838). Both these methods have resulted in a cal_min value of zero as opposed to the negative number I get from using the flirt_average command.
>
> My questions are
> 1. what are cal_min and cal_max values?
> 2. Should I not be using flirt_average because of the negative value I am getting for cal_min?
> 3. Is it ok that the cal_max value is almost double of that of the original input files (although the output file has been averaged)?
>
> Sorry about the long explanations and I appreciate any advice you can provide.
>
> Many thanks
> Reem
>
>
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