Questions regarding preprocessing

[Ariadna Albajara Sáenz]

Dear all, 

 

I am using DTI-TK and I would have some questions regarding the pre-processing: 

1.The fsl_to_dtitk allows converting the eigensystem volumes to DTI-TK compatible volumes. According to the website, the output will be in the correct format and correctly preprocessed. Does this mean that the file “subjectx_dtitk.nii.gz” created is already:

o   Scaled?

o   Non-brain tissue has been removed?

o   Outliers have been removed?

o   Volumes are spd?

o   Volumes have been resampled to share the same voxel space?

 

2.If yes, are these “subjectx_dtitk.nii.gz” files the ones that have to be directly inputted in the following section (bootstrap without an existing sample in my case) or the files “subjectx_dtitk_norm.nii.gz”?

 

3. When checking the tensors as 3D tensor glyphs using TVglyphview, the tensors in the sagittal and coronal images look like stripes in my images (although correctly oriented), but the axial looks fine, as shown in the attached figures. Would someone know how to solve this? And where does the problem come from?

 

Thanks a lot in advance, 

 

Ariadna

[Hui Zhang]

Hi Ariadna,

See my comments below.

Gary

On Sat, Sep 28, 2019 at 9:41 AM Ariadna Albajara Sáenz <ariadna....@gmail.com> wrote:

Dear all, 

 

I am using DTI-TK and I would have some questions regarding the pre-processing: 

1.The fsl_to_dtitk allows converting the eigensystem volumes to DTI-TK compatible volumes. According to the website, the output will be in the correct format and correctly preprocessed. Does this mean that the file “subjectx_dtitk.nii.gz” created is already:

o   Scaled?

o   Non-brain tissue has been removed?

o   Outliers have been removed?

o   Volumes are spd?

o   Volumes have been resampled to share the same voxel space?

Yes, that is intent but worth you making sure these are done correctly for your data.

 

2.If yes, are these “subjectx_dtitk.nii.gz” files the ones that have to be directly inputted in the following section (bootstrap without an existing sample in my case) or the files “subjectx_dtitk_norm.nii.gz”?

Yes but again don't take my word for it.  Take a look at the volumes yourself in fslview.  It will be apparent why you should not use the other volume you mentioned.

 

3. When checking the tensors as 3D tensor glyphs using TVglyphview, the tensors in the sagittal and coronal images look like stripes in my images (although correctly oriented), but the axial looks fine, as shown in the attached figures. Would someone know how to solve this? And where does the problem come from?

They look fine.  The issue you noted reflects the poor through-plane resolution of your data.