> On 3 Nov 2015, at 20:31, Aaron <[log in to unmask]> wrote:
>
>> The first path is within the FSL release package, so check you have FSLDIR set correctly (and exported) before trying hcp_fix. The second path is a FMRIB internal path and I can find no reference to it in the fix 1.06 sources or indeed the compiled code.
> Without being able to find the FSL distro the mc files wouldn't be produced and thus you would see the segmentation fault.
>
> The first path isn't in the neurodebian release. I think the second must be somewhere in the files distributed with fix.. I can't imagine any other possibility.
>
See below.
>>> Octave still doesn't work, it fails at fix_3_clean.m, line 30, column 9.
>> Is this the line that gives the segmentation fault or is there another error message?
>
> The relevant log:
> error: value on right hand side of assignment is undefined
> error: called from:
> error: /usr/local/fix/fix_3_clean.m at line 30, column 9
>
This line loads a text file generated from the specified labelling file, stored in the file .fix). I guess this must be empty, could you confirm that when running under Octave this is the case - the console should have printed something like:
FIX Applying cleanup using cleanup file: XXX and motion cleanup set to YYY
where XXX is the file that is going to be used for generating the contents of .fix.
> Otherwise there are values in 8 columns and some warnings such as:
> warning: function /usr/share/fsl/5.0/etc/matlab/read_pulse.m shadows a core library function
>
>> The compiled scripts work, only i noticed in the log that TR is not correctly set. This is set in hcp_fix (fslval $fmri pixdim4). Somewhere in the pipeline scripts the value gets changed - I checked, it's not in the dicom to nifti conversion. Other folks might want to double check this is correct.
>
> Interestingly, I manually set TR in hcp_fix, in the .fix.log it got switched back to 4 somehow..
>
> ------------------------------------------
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/bin/glnxa64:/usr/local/MATLAB/MATLAB
> _Compiler_Runtime/v83/sys/os/glnxa64
> Warning: Name is nonexistent or not a directory: /usr/local/fmrib/fmt
>> In path at 109
> In startup at 2
>
OK, I guess the compiled version has pulled in a path entry defined in the MATLAB used to compile, this can be ignored it will have no effect on the operation of the program.
> hp =
>
> 2000
>
>
> TR =
>
> 2
>
>
> ------------------------------------------
> Setting up environment variables
> ---
> LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/bin/glnxa64:/usr/local/MATLAB/MATLAB_Compiler_Runtime/v83/sys/os/glnxa64
> Warning: Name is nonexistent or not a directory: /usr/local/fmrib/fmt
>> In path at 109
> In startup at 2
>
> aggressive =
>
> 0
>
>
> domot =
>
> 1
>
>
> hp =
>
> 2000
>
>
> TR =
>
> 4
>
> Elapsed time is 0.865453 seconds.
> Elapsed time is 0.284021 seconds.
>
>
>
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