>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.
>> 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
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
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.
