From dany at biospective.com  Thu Nov 26 08:40:24 2020
From: dany at biospective.com (Dany Chagnon)
Date: Thu, 26 Nov 2020 08:40:24 -0500
Subject: [MINC-users] mincbbox on volume with a scale of 0
Message-ID: <CALN_q7nj6LWqw8cVWC2v3cRTcFMVpDr7siQqFBwGkEzVeqh-QQ@mail.gmail.com>

Dear MINC users,

There seems to be an issue with mincbbox on volumes with a single value,
but with a range of possible voxel values. To reproduce that issue, you can
create a volume with:
1- make_phantom -signed -short -voxel_range -10 100 <template_volume>
2- minccalc -expression '1' <template_volume> <test_volume>
That yields a volume filled with 1s, but with voxel that could range from
-10 to 100. Calling mincbbox on that volume returns "X X X -inf -inf -inf"
where X is 1.8E308. Repeating those same steps, but filling the volume with
values >10 would not have this issue.

As far as I can tell this is because the scale is forced to take a non-zero
value here:
https://github.com/BIC-MNI/libminc/blob/master/volume_io/Volumes/volumes.c#L2537-L2543

I can see two main ways to see that issue:
1) allow the scale to be 0 in libminc
2) rescale the voxel range in minccalc

Best regards,
Dany

From gabriel.devenyi at mcgill.ca  Thu Nov 26 09:37:57 2020
From: gabriel.devenyi at mcgill.ca (Gabriel A. Devenyi)
Date: Thu, 26 Nov 2020 09:37:57 -0500
Subject: [MINC-users] mincbbox on volume with a scale of 0
In-Reply-To: <CALN_q7nj6LWqw8cVWC2v3cRTcFMVpDr7siQqFBwGkEzVeqh-QQ@mail.gmail.com>
References: <CALN_q7nj6LWqw8cVWC2v3cRTcFMVpDr7siQqFBwGkEzVeqh-QQ@mail.gmail.com>
Message-ID: <CAFQOoOq_vproKOwgYES3m-3d2udPmozn5uUqrr0wNxWQ2WstHg@mail.gmail.com>

Hi Dany,

Would you please open an issue on the libminc github. Thanks.



--
Gabriel A. Devenyi Ph.D.
Research Computing Associate
Computational Brain Anatomy Laboratory
Cerebral Imaging Center
Douglas Mental Health University Institute
Affiliate, Department of Psychiatry
McGill University
t: 514.761.6131x4781
e: gabriel.devenyi at mcgill.ca


On Thu, 26 Nov 2020 at 08:40, Dany Chagnon <dany at biospective.com> wrote:

> Dear MINC users,
>
> There seems to be an issue with mincbbox on volumes with a single value,
> but with a range of possible voxel values. To reproduce that issue, you can
> create a volume with:
> 1- make_phantom -signed -short -voxel_range -10 100 <template_volume>
> 2- minccalc -expression '1' <template_volume> <test_volume>
> That yields a volume filled with 1s, but with voxel that could range from
> -10 to 100. Calling mincbbox on that volume returns "X X X -inf -inf -inf"
> where X is 1.8E308. Repeating those same steps, but filling the volume with
> values >10 would not have this issue.
>
> As far as I can tell this is because the scale is forced to take a non-zero
> value here:
>
> https://github.com/BIC-MNI/libminc/blob/master/volume_io/Volumes/volumes.c#L2537-L2543
>
> I can see two main ways to see that issue:
> 1) allow the scale to be 0 in libminc
> 2) rescale the voxel range in minccalc
>
> Best regards,
> Dany
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> https://mailman.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>