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