[Camino-users] Two-tensor Fitting to HCP Data

[Philip A Cook]

Hi,

I just noticed that if you do this, it will break the gradient adjustment that happens if you pass -gradadj.

This isn't a fatal error since most algorithms that normalize DWI data don't use -gradadj anyway. But if you do a linear DT fit with -gradadj, you'll need to use the original scheme file.

On May 27, 2015, at 6:16 PM, Philip A Cook <cookpa at mail.med.upenn.edu> wrote:

> Hi,
> 
> I've just pushed a new option to fsl2scheme to do this:
> 
>  fsl2scheme -bvals hcp.bval -bvecs hcp.bvec -zerobval 5 -bscale 1 > hcp.scheme
> 
> This sets b-values at or below a specified threshold to zero. 
> 
> 
> On May 16, 2015, at 4:11 AM, Alexander, Daniel <d.alexander at ucl.ac.uk> wrote:
> 
>> The simplest thing is just to set all those low b-values to zero in the schemefile.
>> 
>> Danny
>> 
>> 
>>> On 15 May 2015, at 21:45, John Plass <johncplass at gmail.com> wrote:
>>> 
>>> Hello Camino experts,
>>> I was wondering if anyone could help me with processing Human Connectome Project Data with Camino. I've seen 2 previous posts on this topic, but I couldn't find any details on going this far. So far, I've successfully been able to (a) fit single tensors and (b) threshold voxels according to the SH fit, both with spatial variations in b-values being accounted for. Both look great! However, when I try to fit a two-tensor model, I get the following feedback repeatedly:
>>> 
>>> imaging.DW_Scheme normalizeData
>>> WARNING: No b=0 data, cannot normalize
>>> 
>>> I assume this is due to the fact that the b=0 volumes actually have b-values around 5. Is there an easy way to get around this?
>>> 
>>> Any help would be much appreciated!
>>> 
>>> Thanks,
>>> John Plass
>>> 
>>> [For reference, here are the commands I've been using:]
>>> -Single tensor fit
>>> wdtfit dwi.Bfloat hcp.scheme -bgmask nodif_brain_mask.nii.gz -outputfile dt.Bdouble -gradadj grad_dev.nii.gz
>>> 
>>> -Classification (treshold values eyeballed)
>>> voxelclassify -inputfile dwi.Bfloat -schemefile hcp.scheme -order 4 -gradadj grad_dev.nii.gz -ftest 1.0E-50 1.0E-15 1.0E-01 > dwi_VC.Bint
>>> 
>>> -Double tensor fit
>>> modelfit -inputfile dwi.Bfloat -model pospos ldt_wtd -schemefile hcp.scheme -bgmask nodif_brain_mask.nii.gz -gradadj grad_dev.nii.gz > TwoTensorCSymA.Bdouble
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>> 
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> test/ScriptTest.out.billie 
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