Dear Vikram,

Thanks for your reply.  As I said, it might be the version of fieldmap toolbox I use.  my lines 217-220 is virtually only one line of code and if I comment them out I won't have values for ii,jj, nn and pp in later line 223.  I've put in below a screen shot of the code so you know what I'm talking about:

Any idea for my code in particular?

Thanks,

Wei

From: Vikram Rao [mailto:[log in to unmask]]
Sent: Friday, February 24, 2012 9:56 PM
To: Huang, Wei (Psychiatry)
Cc: [log in to unmask]
Subject: Re: [SPM] Field Map Toolbox with Philips images

Hi Wei,

It is actually in the pm_unwrap.m file look out for lines 217-220 ...just comment them out and it worked for me.

Cheers!
Vikram Rao
UC Berkeley, Psychology Dept.
Berkeley, California, USA
"Brain cells come and brain cells go, but fat cells live forever!!"

On Thu, Feb 23, 2012 at 11:54 AM, Wei Huang <[log in to unmask]> wrote:

I got the same error message but maybe because I'm using version 2.1 of Fieldmap toolbox, I don't see the lines of codes Bruno listed below.  However, similar to what Bruno found, tracking back from the error, the following line seems to be what's causing the error:
[ii,jj,nn,pp] = pm_create_connectogram(irima,opm);

After calling pm_create_connectogram(irima,opm), none of the parameters ii,jj,nn and pp had a value.  This subroutine calls a compiled c program (pm_create_connectogram_dtj.c), which made it impossible for me to further debug without the appropriate c compiler.  I've tried on both a 64-bit and a 32-bit windows PC, neither of the mex files worked.

Any other idea?


-Wei

------------------------------------------------------------------------------------------
Re: Field Map Toolbox with Philips images

From:


"Bruno L. Giordano" <[log in to unmask]>


Well,

I actually might have found the problem. Comments welcome.

The call that leads to the error:

upm = pm_merge_regions(opm,irima,ii,jj,nn,pp,rs);

gives in input some empty variables (all of them exception done for opm
and irima).

The empty variables are created by the call to:

[ii,jj,nn,pp] = pm_create_connectogram(irima,opm);

So something might be wrong with what is fed in input to
pm_create_connectogram (irima,opm).

One finds just before the call to this last function a bug fix:

      % Added this little bug fix which prevents pm_merge_regions crashing
      % because it has too many regions to merge.
      while cn>1800 & nstep > 2
          nstep=nstep-1;
          [irima,cn] = pm_initial_regions(opm,mask,nstep);
      end

Commenting out the bug fix actually appears to solve the problem :-)

       Bruno

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
Bruno L. Giordano, PhD
Erasmus Mundus - ACN postdoc @
Voice Neurocognition Laboratory (CCNi, Glasgow Univ) &
Affiliate member of Music Research Dept. (McGill Univ, Montréal)
URL: http://www.brunolgiordano.net

On 01/12/2011 6:27 PM, Bruno L. Giordano wrote:
> Might actually be a good idea to include the original message ;-)
>
> Again: I am getting exactly this error. Did you find the cause? Does
> some kind soul have a suggestion?
>
> Following John's suggestion
> (https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=SPM;d777bd89.0802), I
> commented these lines of code to handle another problem.
>
> elseif any(any(diff(ip_mat,1,1),1))
> errordlg({'Images don''t all have same orientation & voxel size'});
> drawnow;
> varargout{1}=[];
>
> Might that be the cause?
>
> Cheers,
>
> Bruno
>
> On 04/11/2011 4:50 PM, Vayssiere Nathalie wrote:
>> Hi,
>> I try to use the field map toolbox with B0MAp acquired on a philips
>> scanner. I load my images of phase and amplitude and
>> I obtain the following error message when I do calculate:
>>
>> ?? Error using ==> pm_merge_regions
>> pm_merge_regions: i must be a column matrix
>>
>> Error in ==> pm_unwrap at 223
>> upm = pm_merge_regions(opm,irima,ii,jj,nn,pp,rs);
>>
>> Error in ==> pm_make_fieldmap at 166
>> [fm.upm,angvar,fm.mask,fm.opm] = pm_unwrap(cmap,pxs,flags.method);
>>
>> Error in ==> FieldMap at 1623
>> IP.fm = pm_make_fieldmap([IP.P{1} IP.P{2} IP.P{3}
>> IP.P{4}],IP.uflags);
>>
>> Error in ==> FieldMap at 699
>> status=FieldMap('CreateFieldMap',IP);
>>
>> ??? Error while evaluating uicontrol Callback
>>
>> Has someone an idea of what is wrong with my images???
>>
>> Thank you very much for your help
>>
>> Nathalie