[MINC-users] mritoself xcorr memory problem

[Andrew Janke]

Whoops, make that

   Minc + hdf

Andrew (who needs to be more carefull when using nokias predictive text...)

On 2010-07-01, Andrew Janke <a.janke at gmail.com> wrote:
> Hi mishkin
>
> This memory issue is known to happen with the current mincmorph + hdf
> combination.  It is due to a combination of chunking sizes and file
> size.
>
> You will find that it is not due to filetype but the size of the file
> itself.  This is of course assuming the problem is what I think it is.
>
> This problem is fixed in mincmorph 2.1 which is due for release either
> this week or early next week.
>
> Andrew.
>
> On 2010-06-23, Mishkin Derakhshan <mishkind at gmail.com> wrote:
>> Hi,
>> I have found that every now and then when I run mritoself with the
>> xcorr option it will take up as much memory as it can find and never
>> complete.
>>
>> I've managed to narrow the problem down to a data type problem,
>> specifically if my source image is of type long.
>> In this case, mritoself, or more precisely volume_stats according to
>> top, will just eat up all 8GB of my memory.
>>
>> This fails:
>> mritoself brain.mnc.gz head.mnc.gz out.xfm -clobber -xcorr
>>
>> where mincinfo brain.mnc.gz gives:
>> file: brain.mnc.gz
>> image: signed__ long -2147483648 to 2147483647
>> image dimensions: zspace yspace xspace
>>     dimension name         length         step        start
>>     --------------         ------         ----        -----
>>     zspace                     60            3          -48
>>     yspace                    256     0.976562     -100.586
>>     xspace                    256     0.976562     -124.023
>>
>> Whereas if I do this, then it works:
>> mincresample brain.mnc.gz -short short.mnc
>> mincinfo short.mnc
>> file: short.mnc
>> image: signed__ short -32768 to 32767
>> image dimensions: zspace yspace xspace
>>     dimension name         length         step        start
>>     --------------         ------         ----        -----
>>     zspace                     60            3          -48
>>     yspace                    256     0.976562     -100.586
>>     xspace                    256     0.976562     -124.023
>>
>> mritoself short.mnc head.mnc.gz out.xfm -clobber -xcorr
>>
>>
>> I've managed to find a fix for my problem but perhaps someone with a
>> bit more knowledge of what is going on can fix this bug (or feature
>> depending on what you wnt to call it).
>>
>> mishkin
>>
>> fyi:
>>
>> opus[~]$ uname -a
>> Linux opus 2.6.24-24-generic #1 SMP Tue Aug 18 16:22:17 UTC 2009
>> x86_64 GNU/Linux
>>
>> opus[~]$ mritoself -version
>> mritoself 0.99.3 built from:
>> Package mni_autoreg 0.99.3, compiled by ladmin at ccr-twodogs
>> (x86_64-unknown-linux-gnu) on Wed Feb 11 10:46:24 EST 2009
>>
>> opus[~]$ mincinfo -version
>> program: 2.0.17
>> libminc: 2.0.17
>> netcdf : "3.6.2" of Feb  8 2008 15:52:05 $
>> HDF5   : 1.6.5
>> _______________________________________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>>
>