[MINC-users] EMMA tools for Cygwin

[Pierre Bellec]

Dear Paul,

Sorry for taking so long to jump in. I tested the niak reader and writer of
MINC on cygwin years ago, but I ran into various issues at the time. Since
MINC was not officially supported on this platform, I decided to abandon
windows altogether and assume people would install a ubuntu virtual machine
if they needed to read/write minc. I am thus very happy to see you managed
to get it to work, that's great news. However, the change you suggested is
what's in the code already.
http://code.google.com/p/niak/source/browse/trunk/commands/read_write/niak_read_hdr_minc.m

Maybe you were working on a version that had been edited for windows but
somehow ended up breaking things with cygwin.

Best,

Pierre Bellec, PhD
Research Centre of the Montreal Geriatric Institute
& Department of Computer Science and Operations Research
University of Montreal, Québec, Canada
http://simexp-lab.org/brainwiki/doku.php?id=pierrebellec
(001)(514) 340 3540 #3367


2012/7/26 Paul GRAVEL <pgravel at bic.mni.mcgill.ca>

> Hi All!
>
> I think I got it!
>
> Line 87 of niak_read_hdr_minc.m was modified from:
> [flag,str_header] = system(cat(2,'mincheader.exe ',file_name));
>
> to:
>
> [flag,str_header] = system(cat(2,'bash -c "mincheader ',file_name,'"'));
>
> so it ensures calling the mincheader command using cygwin's bash, instead
> of windows.
>
> Many thanks again!
>
> Paul
>
>
>
> On Thu, 26 Jul 2012, Paul GRAVEL wrote:
>
>  Many Thanks Claude!
>>
>> Unfortunately, I still have the same problem with mincheader, and indeed
>> it seems to be the 64-bit architecture that is causing the problem... But
>> the question remains: why would it run fine in Cygwin (which is installed
>> on the Windows XP x64 machine), but not when called via Windows, while
>> tools like mincinfo runs fine in both cygwin and matlab?
>>
>> In the meantime I will verify if there is a way to call commands from
>> matlab by specifying a 32-bit flag...
>>
>> Best,
>>
>> Paul
>>
>> On Thu, 26 Jul 2012, Claude LEPAGE wrote:
>>
>>  Paul,
>>>
>>>  I think someone has asked the following question previously, but just to
>>>> bu sure: where can I find the latest MINC source files to be recompiled
>>>> for Cygwin?
>>>>
>>>
>>> I have some here:
>>>
>>> http://www.bic.mni.mcgill.ca/**users/claude/cygwin_nt-5.1-1.**7.7.tar.gz<http://www.bic.mni.mcgill.ca/users/claude/cygwin_nt-5.1-1.7.7.tar.gz>
>>>
>>> Basic minc tools, but likely enough for most users. This is a
>>> non-official
>>> package. Use at your own risks. It's 32 bits.
>>>
>>> Claude
>>>
>>> ______________________________**_________________
>>> MINC-users at bic.mni.mcgill.ca
>>> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
>>>
>>>  ______________________________**_________________
>> MINC-users at bic.mni.mcgill.ca
>> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
>>
>>  ______________________________**_________________
> MINC-users at bic.mni.mcgill.ca
> http://www.bic.mni.mcgill.ca/**mailman/listinfo/minc-users<http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users>
>