Hey fslexperts, hey Stam
thank you for your request.
So I know how the spherical angles are defined but I still do not get to
know how I can get from the bedpostx output the angle information from a
single dyad. I want to estimate the accuracy of the direction information
(dyads/voxel) for different measurements (b-values) in a given roi.
Therefore I need a kind of reference value so that I can compare the
direction information within a voxel for different measurements. I was
thinking maybe it is the easiest to calculate the spherical angles of each
dyads/voxel and compare them thus I can say something about my accuracy and
precision.
So it would be nice if somebody has another good approach or idea how to
compare measurements (different b-values) regarding to the direction
information in a given roi or can tell me how to get the angles as values
of a given dyad.
Anyway thank you again.
Best
Max
2016-11-14 12:46 GMT+01:00 Stamatios Sotiropoulos <
[log in to unmask]>:
> Hi Max
>
> The dyads is the only information you need for visualisation.
>
> If you indeed need the angles for some reason, then theta and phi are the
> spherical angles in radians. These are defined as in the sketch that Saad
> sent, i.e phi is the angle from a reference axis on the xy plane and theta
> is the angle from that plane.
>
> Finally, if you need to read values out of a nifti file, then in general
> you can either use Matlab or use fslmeants —showall.
>
> Hope this helps
> Stam
>
>
> On 14 Nov 2016, at 11:07, mangan bvb <[log in to unmask]
> <[log in to unmask]>> wrote:
>
> Hi and thank you again for your help,
> but for me this looks like a code which represents the transformation
> between spherical and cartesian coordinate system. Sorry but I don't know
> how I can use this code to get my direction information (angles ind rad or
> degree) from my dayds (ph1samples, th1samples files)? I still do not
> understand how I get the angle values of my dayds? In addition I do not
> understand the files ph1samples, th1samples. In the documentation it is
> said that these files including the angle information for the dayds? But
> how is it possible to read them out of a nifti file such as ph1samples,
> th1samples.
> Thank you
> Best
> Max
>
>
> 2016-11-12 11:29 GMT+01:00 Saad Jbabdi <[log in to unmask]>:
>
>> Hi - This is the bit of code in FSL that carries out the transformation.
>>
>> In the below, “dir” is the dyadic vector and (th,ph) are the polar
>> angles.
>>
>> I hope that clarifies things?
>>
>> Cheers
>> Saad
>>
>>
>> void cart2sph(const ColumnVector& dir, float& th, float& ph)
>> {
>> float mag=sqrt(dir(1)*dir(1)+dir(2)*dir(2)+dir(3)*dir(3));
>> if(mag==0){
>> ph=M_PI/2;
>> th=M_PI/2;
>> }
>> else{
>>
>> if(dir(1)==0 && dir(2)>=0) ph=M_PI/2;
>> else if(dir(1)==0 && dir(2)<0) ph=-M_PI/2;
>> else if(dir(1)>0) ph=atan(dir(2)/dir(1));
>> else if(dir(2)>0) ph=atan(dir(2)/dir(1))+M_PI;
>> else ph=atan(dir(2)/dir(1))-M_PI;
>>
>> if(dir(3)==0) th=M_PI/2;
>> else if(dir(3)>0) th=atan(sqrt(dir(1)*dir(1)+dir(2)*dir(2))/dir(3));
>> else th=atan(sqrt(dir(1)*dir(1)+dir(2)*dir(2))/dir(3))+M_PI;
>> }
>> }
>>
>>
>>
>>
>>
>>
>> On 12 Nov 2016, at 08:16, mangan bvb <[log in to unmask]
>> <[log in to unmask]>> wrote:
>>
>> Hi Saad,
>> thank you for this information, but this image explains just spherical
>> coordinates and not how I can get the angle values from the data.
>> Has somebody else an idea?
>> Best,
>> Max
>>
>> 2016-11-10 15:58 GMT+01:00 Saad Jbabdi <[log in to unmask]>:
>>
>>> Hi
>>> This page explains how the angles relate to the dyads:
>>> https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FDT/UserGuide?
>>> action=AttachFile&do=view&target=fdt_spherical_polars.gif
>>>
>>>
>>> Cheers
>>> Saad
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 10 Nov 2016, at 14:29, Max Wichmann <[log in to unmask]
>>> <[log in to unmask]>> wrote:
>>>
>>> Dear all,
>>> I'm new to Fsl and in general to neuroscience so I already say sorry if
>>> my question is not that precisely.
>>> Anyway this is my question:
>>>
>>> I would like to compare the direct information (dyads) for different
>>> measurements (b-values). Therefore I need to know the scalar value of the
>>> two angles presenting the orientation of one dyad in a voxel.
>>>
>>> 1. So first of all is it right that ph1samples, th1samples presenting
>>> the angles in spherical coordinates for dayd1 which can be understand as
>>> the main direction in a given voxel?
>>> 2. How can I find out the the scalar values of both angles given in one
>>> voxel?
>>>
>>> I tried to open the ph1samples, th1samples in fslview and check the
>>> histogram. But actually I do not understand the distribution. I was
>>> thinking the x-axis represents the different angles and the y-axis their
>>> related frequency. But I cant find some information in that distribution
>>> about the given angles. Maybe the scaling is weird. But I also changed it
>>> to something like -pi to pi or -180 to 180. But still the meaning is not
>>> clear.
>>>
>>> So I guess I have some false idea about the outputs? Maybe somebody can
>>> help me with this?
>>>
>>> Thank you very much
>>>
>>> best
>>>
>>> Max
>>>
>>>
>>>
>>
>>
>
>
