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Warning message during Creation of a population template

Submitted by CadyWang on
Category
DRTAMAS

Hello,

I have some questions of some warning messages I got during creation of a population template. I  want to create a template out of 50 subjects using TORTOISE 3.2 in Ubuntu 20.04.  The command I used is follows:  dtireg_create_template -s=sus.txt -n=1 -c=1 -r=1.5x1.75x2.5.  Though the procedure ran through and displayed the completion message, I also got several warnings as shown below:

warnings

If create a template out of 4 subjects , these warnings will disappear completely.

Submitted by irfanogl on Fri, 07/16/2021 - 12:24

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Hello,

The number of subjects should not matter. We have created templates out of 1000s of subjects.

I see a couple of issues here. (Some related, some are not)

1) DRTAMAS always outputs isotropic voxel size so a resolution of type  -r=1.5x1.75x2.5.  is not accepted.  it should be "-r 1.5"   to have the outputs be at 1.5mm isotropic resolution.

2) At the begininng, when reading tensors, all the tensors are named "tortoiset_aff.nii"   , this generally indicates a problem with the text file sus.txt.  Are all the lines "tortoiset.nii"  ?

3) A spacing of 0 is not allowed.     The resolution of the input files seem to be weird. Are these tensors, specifically tortoiset.nii computed by TORTOISE?  I mean did you use an executable like EstimateTensorWLLS or  EstimateTensorNLLS?

The resolution of a tensor image should be of the form   resx  x  resy  x  resz  x 1
The tensors computed by TORTOISE executables would already be in this form.

Let us know.

 

Submitted by irfanogl on Wed, 08/04/2021 - 12:00

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Hello again,

Q2) I am glad it is solved.

Q3) This should be fine normally unless either DIPY or the conversion tool outputs the 4th dimension as 0. So what I suggest is to run the TORTOISE executable Set4DImageResolution.

If the original tensor is aaa_DT.nii with resolution 1.5x1.75x2.5x0,   you run it by:

Set4DImageResolution aaa_DT.nii aaa_DT.nii 1.5 1.75 2.5 1  (last parameter is 1 instead of 0)

Hopefully, after this they should be compatible.

Q1)  Unfortunately, DRTAMAS is not designed for anisotropic resolution. So it will always output at isotropic resolution so I storngly suggest to use "-r 1.5"

However, after the template is created, you can resample it with the command ResampleTensor.

You can run it by:   ResampleImage average_template_diffeo_6.nii 1.5 1.75 2.5

and your new template will have the desired resolution.

 

Q4) Apologies but I did not fully understand your last question, What do you mean by "split the ROI area?

 

Hope these help.