superimposition of native results and native T1 image

[IFaillenot]

Bonjour,

I used Vol2brain to detect white matter lesion/abnormalities in a patient. This was well detected.
When the mni_tissue label 8 ("lesion") is overlayed on the mni_t1 image (left part of the figure joined) , it is perfect.
When the native_tissue label 8 is overlayed on the T1 image given as input to vol2brain (right part of the figure), we can see that this T1 is not the "native" image...
the readme file says "{native, mni}t1<JOB_ID>.nii.gz Filtered and normalized T1 image"
but there isn't native_t1_* image in the directory.

[pierrickvolbrain]

I guess that the issue is coming from your viewer which do not correctly read the matrix header. With ITKSnap (the viewer recommended in the tutorial), your case seems perfect.

[IFaillenot]

usually, MRIcro_GL correctly reads the matrix header....
I am quite self confident about the format (Siemens data acquired this year, converted in bids with heudiconv)
where did you find the "original_t1_job* image or the "native_t1_job* ? it will solve the issue if I have it

[pierrickvolbrain]

This is the submitted image. I will send it to you by PM.

"the readme file says "{native, mni}t1<JOB_ID>.nii.gz Filtered and normalized T1 image" : this was true, but finally we decided to remove it in order to reduce the size of the archive. We will update the readme.

[IFaillenot]

ok the original is exactly the same that mine.
So I still have a problem.