DTI-TK/TBSS plugin - a issue with generating 1mm^3 template

[yj.ell...@gmail.com]

Hi all DTI-TK experts,

I'm trying to integrate DTI-TK normalization and TBSS. However, I ran into a problem. 

The problem is when I try ' TVMean -in subjs_normalized.txt -out mean_final_high_res.nii.gz' after I compute '~_combined.df.nii.gz' file. It says the number of components of the file (_combined.df.nii.gz) is 3, so they can not create mean_final_high_res template. So I checked all files and realized my '~_aff_diffeo.df.nii.gz' has only 3 components. The other normalized files '~_aff_diffeo.nii.gz' have 6 components though. Is this because my _aff_diffeo.df.nii.gz makes _combined.df.nii.gz as 3 components? 

I couldn't find others who seem having the same problem with me. I checked the log and it seems there was no error when it ran diffeomorphic normalization. 

Could someone please let me know what you think or the step I should check? 

Sincerely,

Elle 

[Hui Zhang]

Hi Elle,

The problem is most likely caused by including ~_aff_diffeo.df.nii.gz in your subjs_normalized.txt.  In the latter file, it should only contain ~_aff_diffeo.nii.gz.

Gary

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[Ariadna Albajara Sáenz]

Dear all, I am reopening this post because I have a related issue. After running this command "dti_warp_to_template_group subjs.txt mean_final.nii.gz 1 1 1" I have two kinds of image outputs: "subj_dtitk_diffeo.nii.gz" and "subj_dtitk_ciombined.df.nii.gz" but not "~_aff_diffeo.nii.gz", which are the ones supposed to go in the "subjs_normalized.txt". 

Would someone know if this is normal and which images should go in the file "subjs_normalized.txt"? Thank you in advance, 

Ariadna

El lunes, 19 de febrero de 2018, 13:17:45 (UTC+1), Gary escribió:

Hi Elle,

The problem is most likely caused by including ~_aff_diffeo.df.nii.gz in your subjs_normalized.txt.  In the latter file, it should only contain ~_aff_diffeo.nii.gz.

Gary

On Tue, Feb 13, 2018 at 6:19 PM, <yj.el...@gmail.com> wrote:

Hi all DTI-TK experts,

I'm trying to integrate DTI-TK normalization and TBSS. However, I ran into a problem. 

The problem is when I try ' TVMean -in subjs_normalized.txt -out mean_final_high_res.nii.gz' after I compute '~_combined.df.nii.gz' file. It says the number of components of the file (_combined.df.nii.gz) is 3, so they can not create mean_final_high_res template. So I checked all files and realized my '~_aff_diffeo.df.nii.gz' has only 3 components. The other normalized files '~_aff_diffeo.nii.gz' have 6 components though. Is this because my _aff_diffeo.df.nii.gz makes _combined.df.nii.gz as 3 components? 

I couldn't find others who seem having the same problem with me. I checked the log and it seems there was no error when it ran diffeomorphic normalization. 

Could someone please let me know what you think or the step I should check? 

Sincerely,

Elle 

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[Hui Zhang]

Hi Ariadna,

The files to use are the ones ending with *diffeo.nii.gz.  Have you taken a look at these files with fslview?  It is important that you do that.  If you take a look at the ones ending with *combined.df.nii.gz, you will see that they aren't images of brain.  The answer to your question becomes obvious.

Gary

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