Thanks for the suggestion, I tried it with a low number of iterations, and
was able to get some results.
This will be my backup, if this issue can't be resolved.
It would be great if it could work with octave, since I plan on using PALM
with large datasets in the near future.
Thanks,
-Arnold
On Mon, Nov 5, 2018 at 8:51 AM Anderson M. Winkler <[log in to unmask]>
wrote:
> Hi Arnold,
>
> Have you fixed the problem? If not, and if you have FreeSurfer or FSL
> installed, you may try the option -noniiclass. This will require a lot more
> memory and it will be less efficient, but if nothing else seems to be
> working on your system, maybe that could be an option to get you going...
>
> All the best,
>
> Anderson
>
>
> On Thu, 1 Nov 2018 at 14:51, melanni nanni <[log in to unmask]> 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]>
>> 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]>> 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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