Stable AFQ MATLAB and SPM versions? and AFQ: Error in dtiRawCheckTensors(). Number of array dimensions must match for binary array op

[Rodrigo Perea]

(from: https://github.com/vistalab/vistasoft/issues/246 ) 

Hi, 

The short question:

Could anybody tell me what stable versions your lab is using (e.g. Matlab and spm) when running AFQ successfully. I tend to think (my longer) question below could be  fixed if I try similar stable versions.

The longer question:

I am trying to run AFQ using the branch matlab2017a of vistasoft. So far, I was able to create the tensors but my code breaks when checking the tensor output in dtiInit() when accessing the function dtiRawCheckTensors():

Error using  >
Number of array dimensions must match for binary array op.


Error in mrAnatHistogramClip (line 42)
img(img>upperClipVal) = upperClipVal;


Error in dtiRawCheckTensors (line 88)
t1Im = uint8(round(mrAnatHistogramClip(t1Im,0.4,0.98).*(1-faIm).*255));


Error in dtiInit (line 288)
[pddT1,tmp,mm] = dtiRawCheckTensors(fullfile(dwParams.dt6BaseName,'bin',...

```

If I debug the code and go to  `dtiRawCheckTensors`, I notice that after executing `mrAnatResliceSpm()` the values for `faIm` (line 85) and `t1Im` (line 87) are assigned empty arrays (check below). My gut tells me that something is happening with my `bb` variable (in line 78) as row 2 col 1 and 2 are negative and < than row 1. Or could it be something else? I tried this with 3 different datasets and I still keep getting the error :/ 

bb =
85.2203 129.7039 111.6288
-80.2502 -87.3959 -132.5730

t1Im = 

Empty array: 166-by-218-by-0

faIm =


 Empty array: 166-by-218-by-0

Any help will be appreciate it. Thanks,

Rodrigo

  

**My additional question:

Could it be a matlab/spm/fsl version problem? If so, could somebody comment on the versions they use when the code converges?

I am using:

Matlabv2016a, SPM8, FSL5.0.9

[Jason Yeatman]

I've never seen this error before

Have you ac-pc aligned your images or at least set the origin in a reasonable manner?

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