Can you use interpreted matlab?  Do you have GIFTI installed?  Also, the 7T data already have FIX run on them.

 

Matt.

 

From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of "Niels Janssen ." <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Friday, November 8, 2019 at 2:55 AM
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Fix on hcp data

 

Dear HCP masterminds,

 

I am trying to get Fix (v1.068) to work on single subject HCP data. Fix steps 1 and 2 work, I am running into problems with the final step (cleaning). I have Ubuntu Server 18.04, Workbench 1.4.1, Matlab Runtime Compiler v93. 

 

I run:

/usr/local/fix/fix -a rfMRI_REST1_7T_PA_hp2000.ica/to_remove.txt -m -h 2000 -A

 

Where 'to_remove.txt' is the output of 'tail -n 1 fix4melview_HCP7T_hp2000_thr10.txt'

 

output of .fix.log:

------------------------------------------------

Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:
/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64

aggressive =   1
domot =    1
hp =     2000
TR =   1
Undefined function or variable 'gifti'.
Error in ciftiopen (line 34)
Error in fix_3_clean (line 46)
MATLAB:UndefinedFunction

 

----------

Furthermore, some additional info when I directly run:

/usr/local/fix/compiled/Linux/x86_64/run_fix_3_clean.sh /usr/local/MATLAB/MATLAB_Runtime/v93  '.fix' 1 1 2000  >> .fix.log2 2>&1

 

output of .fix.log2:

------------------------------------------
Setting up environment variables
---
LD_LIBRARY_PATH is .:/usr/local/MATLAB/MATLAB_Runtime/v93/runtime/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/bin/glnxa64:/usr/local/MATLAB/MATLAB_Runtime/v93/sys/os/glnxa64:
/usr/local/MATLAB/MATLAB_Runtime/v93/sys/opengl/lib/glnxa64
aggressive = 1
domot =   1
hp =    2000
TR =   1
/bin/bash: -cifti-convert: command not found
Undefined function or variable 'gifti'.
Error in ciftiopen (line 34)
Error in fix_3_clean (line 46)
MATLAB:UndefinedFunction

 

I am stuck here, perhaps wb_command is not working? I also realize I could just do 'fsl_regfilt' at this point but I would like to see this working till the end...

 

Thanks again, I am learning a lot!

 

Niels

 

 

--

Niels Janssen

Brain Imaging Laboratory

Institute of Biomedical Technologies

Institute of Neurosciences

University of La Laguna

Tenerife, Spain

 

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