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On Tue, Nov 6, 2018 at 6:28 AM Flandin, Guillaume <[log in to unmask]> wrote:

Hi Arnold and Melanni,

I still cannot make sense of the errors you report. In order to compile
MEX files for Octave, you indeed need to install liboctave-dev, which
will provide the mkoctfile command.

In a terminal (not within Octave), do the following:
* cd PALM/fileio/@file_array/private/
* rm *.mex*
* mkoctfile --mex file2mat.c
mkoctfile --mex mat2file.c
mkoctfile --mex init.c
This should have created three files with a .mex extension.

Run Octave/PALM and let us know what happens.

Best regards,
Guillaume.

On 01/11/2018 18:50, melanni nanni wrote:
> Hi Arnold,
>
> I also observed that it was a mkoctfile dependent on the version of gcc
> in my case, I installed liboctave-dev, then compile it from terminal.
>
> Best,
>
> Melanni
>
> ------------------------------------------------------------------------
> *De:* FSL - FMRIB's Software Library <[log in to unmask]> en nombre de
> Arnold Evia <[log in to unmask]>
> *Enviado:* jueves, 1 de noviembre de 2018 07:19 p. m.
> *Para:* [log in to unmask]
> *Asunto:* Re: [FSL] Error in mat2file using Palm
>
> I am compiling for Octave on Ubuntu 16.04. When I compiled the file for
> Octave in the terminal, compilation completed with no errors or
> warnings, and I still had the problem.
> I also tried compiling without the 'platform=octave' tag, hoping to get
> some information on what could be going wrong.
>
> -Arnold
>
>
> On Thu, Nov 1, 2018 at 7:28 AM Flandin, Guillaume <[log in to unmask]
> <mailto:[log in to unmask]>> wrote:
>
> Hi Arnold,
>
> Are you compiling for MATLAB or Octave? The issue observed by Melanni
> was with Octave. Here you are compiling with mex from the terminal, so
> it is aiming at compiling for MATLAB (*.mexa64).
> Also, which version of Ubuntu are you using?
>
> Best regards,
> Guillaume.
>
>
> On 31/10/2018 19:59, Arnold Evia wrote:
> > Compiling the file using terminal didn't make a difference.
> > Still observe the same behavior.
> >
> > I tried compiling without the platform tags, and got the
> following result:
> >
> > rm -f file2mat.mexa64 mat2file.mexa64 init.mexa64
> > mex -O -largeArrayDims file2mat.c
> > Building with 'gcc'.
> > Warning: You are using gcc version '5.5.0'. The version of gcc is not
> > supported. The version currently supported with MEX is '6.3.x'. For a
> > list of currently supported compilers see:
> > https://www.mathworks.com/support/compilers/current_release
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > MEX completed successfully.
> > mex -O -largeArrayDims mat2file.c
> > Building with 'gcc'.
> > Warning: You are using gcc version '5.5.0'. The version of gcc is not
> > supported. The version currently supported with MEX is '6.3.x'. For a
> > list of currently supported compilers see:
> > https://www.mathworks.com/support/compilers/current_release
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > MEX completed successfully.
> > mex -O -largeArrayDims init.c
> > Building with 'gcc'.
> > Warning: You are using gcc version '5.5.0'. The version of gcc is not
> > supported. The version currently supported with MEX is '6.3.x'. For a
> > list of currently supported compilers see:
> > https://www.mathworks.com/support/compilers/current_release
> <https://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.mathworks.com%2Fsupport%2Fcompilers%2Fcurrent_release&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=Ox1tpl%2BJnhPz9imCFSqVX0Vi%2BSeP%2B6xdkc6cdZabFdM%3D&reserved=0>.
> > MEX completed successfully.
> >
> > Is mkoctfile dependent on the version of gcc?
> > If so, then I will try again after updating gcc.
> >
> > Arnold M. Evia, Ph.D.
> > Senior Research Associate
> > Department of Biomedical Engineering
> > Medical Imaging Research Center
> > Illinois Institute of Technology
> > http://www.iit.edu/~mri/
> <https://nam04.safelinks.protection.outlook.com/?url=http:%2F%2Fwww.iit.edu%2F~mri%2F&data=02%7C01%7C%7C9bbc52f66f2b4b02446108d640268c98%7C84df9e7fe9f640afb435aaaaaaaaaaaa%7C1%7C0%7C636766931638843783&sdata=JhxZ6Y0BLpowwAZsauK6yOmJj%2FfMD2wWCPDUhPQYxvY%3D&reserved=0>
> >
> >
> > On Wed, Oct 31, 2018 at 7:37 AM Flandin, Guillaume
> <[log in to unmask] <mailto:[log in to unmask]>
> > <mailto:[log in to unmask] <mailto:[log in to unmask]>>> wrote:
> >
> > Hi Arnold,
> >
> > Thanks, we went down the same road with Melanni last week,
> and, while I
> > am still trying to understand what the problem is (somehow
> related to
> > memory alignment), the issue was disappearing if the MEX file were
> > compiled from a terminal:
> >    mkoctfile --mex mat2file.c
> > instead of invoking mex() within octave:
> >    mex mat2file.c
> > It shouldn't make any difference (check the source code of
> mex.m) but
> > apparently it does... I would be curious if you can reproduce
> the same
> > phenomenon.
> >
> > Best regards,
> > Guillaume.
> >
> >
> > On 30/10/2018 21:33, Arnold Evia wrote:
> > > Hello Guillaume and Melanni,
> > >
> > > I am also having the same issue as Melanni using PALM in Ubuntu.
> > > I tried the commands that you suggested, and got the same output
> > as Melanni.
> > >
> > > After some debugging, I may have found a clue as to what's
> happening.
> > > In mat2file.c, I placed a few print statements for some
> variables
> > right before the error message (line 252):
> > >
> > > printf("code = %d\n",map->dtype->code);
> > > printf("bits = %d\n",map->dtype->bits);
> > > printf("channels = %d\n",map->dtype->channels);
> > >
> > > if (map->dtype == NULL) mexErrMsgTxt("Unrecognised
> > 'dtype' value.");
> > > if (map->dtype->bits % 8) mexErrMsgTxt("Can not yet
> write
> > logical data.");
> > > if (map->dtype->channels != 1) mexErrMsgTxt("Can not yet
> write
> > complex data.");
> > >
> > > The program returned unusual numbers:
> > >
> > > code = 16
> > > bits = 32726
> > > channels = 7
> > > Error using subsasgn>subfun
> >
>   ([log in to unmask]:168)
> > > mat2file: Can not yet write logical data.
> > >
> > > Running the program again with the same parameters, values for
> > code and channels stays constant, but the value for bits would
> change:
> > >
> > > code = 16
> > > bits = 32696
> > > channels = 7
> > > Error using subsasgn>subfun
> >
>   ([log in to unmask]:168)
> > > mat2file: Can not yet write complex data.
> > >
> > > As you can see, sometimes bits will be divisible by 8, and the
> > program returns a different error.
> > > There is a table in the script that defines the values for bits,
> > and channels for a specific code.
> > > In this case, bits should be 32, and channels should be 1.
> > > I don't know why bits and channels are being set to incorrect
> > values, and I hope this sheds some light.
> > >
> > > -Arnold Evia
> > >
> >
> > --
> > Guillaume Flandin, PhD
> > Wellcome Centre for Human Neuroimaging
> > UCL Queen Square Institute of Neurology
> > London WC1N 3BG
> >
>
> --
> Guillaume Flandin, PhD
> Wellcome Centre for Human Neuroimaging
> UCL Queen Square Institute of Neurology
> London WC1N 3BG
>
>
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--
Guillaume Flandin, PhD
Wellcome Centre for Human Neuroimaging
UCL Queen Square Institute of Neurology
London WC1N 3BG

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