[MINC-users] EMMA tools for Cygwin

[Paul GRAVEL]

Many thanks Andrew!

I did install the NIAK tools and added the path(s) in Matlab, but I now 
face another problem. When I run the niak_read_minc (in Matlab) command, I 
get the following error message:

##################################################
??? Error using ==> niak_read_hdr_minc at 96
niak:read: Could not parse the minc header !

Error in ==> niak_read_minc at 70
hdr = niak_read_hdr_minc(file_name);
##################################################

where line 96 of niak_read_hdr_minc is returning an error baseb on line 87 
which is:
[flag,str_header] = system(cat(2,'mincheader ',file_name));

When I run this command from Matlab:
file_name = 'qfal_003_0_pet_fr1_32_sm9mm_VoWal_basFunc_k2.mnc'
[flag,str_header] = system(cat(2,'mincheader ',file_name))

I get the following error message:
##################################################
flag =

      1


str_header =

'mincheader' is not recognized as an internal or external command,
operable program or batch file.
##################################################

while it runs fine in cygwin. And yes I have added the cygwin and MINC 
tools paths (C:\cygwin\bin;C:\cygwin\usr\local\mni\bin) to my Windows XP 
path environment variable. For example, when I call mincinfo from within 
Matlab, it runs fine.

In addition, I have noticed that when I do an long listing of the MINC 
tools folder from cygwin: ls -l /usr/local/mni/bin
Most of the MINC tools have the .exe extension, e.g. mincinfo.exe, while 
mincheader does not. I renamed mincheader to mincheader.exe but it did not 
fix the problem. However, the error message in Matlab differed: 
##################################################
flag =

      1


str_header =

The image file C:\cygwin\usr\local\mni\bin\mincheader.exe is valid, but is 
for a machine type other than the current machine.
##################################################

Could this be a result of how it was compiled, and thus cause the error 
explained above? And if so, is there another version of mincheader that 
could solve this problem?

I am using the following MINC tools package:
http://packages.bic.mni.mcgill.ca/cygwin/mni-2006-11-15.tar.gz

and I am running MATLAB Version 7.10.0.499 (R2010a)

Any help will be greatly appreciated!

Best Regards,

Paul


On Wed, 25 Jul 2012, Andrew Janke wrote:

> Hi Paul
>
> On 25 July 2012 01:20, Paul GRAVEL <pgravel at bic.mni.mcgill.ca> wrote:
>> Is there any version of the emma tools for cygwin?
>
> Not that I know of.  In any case EMMA has been deprecated for quite
> some time now in favour of Pierre Bellecs NIAK python package
>
>   http://code.google.com/p/niak/
>
>
> a
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