[MINC-development] mincresample issue/bug at smaller voxel sizes using concatenated transforms

[Alex Zijdenbos]

I agree... ugly. This doesn't seem like something that should be
handled by an environment variable, and not even a command-line option
(although the latter would allow for easier scripting around it). I'll
happily admit that I am not familiar with the innards of mincresample;
but conceptually I would say mincresample should "just work"
regardless of voxel size - which I think leads back to the "ideal"
solution that Claude pointed out - making ftol somehow dependent on
voxel size. If that is not possible, would it work to set it it to a
fixed but very small value that would work across the expected range
of resolutions?

As a side note, I have worked my way around issues like this by
scaling the images up to a ~1mm voxel size, registering and resampling
there, then scaling the voxel size back.

-- A

On Thu, Jan 6, 2011 at 4:17 PM, Andrew Janke <a.janke at gmail.com> wrote:
> Nope, you're not missing anything. It would require an API change (or
> adding a copy of the same function with _ftol(... or something added
> to the end). I am just very adverse to making the result of a MINC
> analysis dependent on an environment variable.
>
> It's just too hidden.  What would be the plan for distributing scripts
> that work on mouse data?  A line in a script that first sets/overrides
> an ENV variable?  ack.
>
>
> a
>
> On 6 January 2011 23:14, Jason Lerch <jason at phenogenomics.ca> wrote:
>> But that would require an API change, wouldn't it? Unless the command line switch to mincresample changes that environment variable ... Or am I missing something too obvious due to lack of coffee?
>>
>> Jason
>>
>> On 2011-01-06, at 12:37 AM, Andrew Janke <a.janke at gmail.com> wrote:
>>
>>> Perhaps it's time for YACLA for mincresample?
>>>
>>> I like this approach more than an environment variable as it will
>>> preserve operation when scripts are passed around.
>>>
>>>
>>> YACLA - Yet Another Command Line Argument
>>>
>>> --
>>> Andrew Janke
>>> (a.janke at gmail.com || http://a.janke.googlepages.com/)
>>> Canberra->Australia    +61 (402) 700 883
>>>
>>>
>>>
>>>
>>> On 24 December 2010 02:48, Matthijs van Eede <matthijs at phenogenomics.ca> wrote:
>>>> Initially I thought the current solution in minc 2.1 would work for use, but
>>>> we quite frequently use transformation grids with resolutions that are a lot
>>>> coarser than the volumes we transform with them, so we would still run into
>>>> the same problem. Is it possible to have an environment variable that can
>>>> override the value that is set for ftol?
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