Summary of what happened:
I ran MELODIC on a set of my own data and manually labeled the components of 10 subjects as either signal or noise. I’m now trying to use FSL FIX to automatically classify the components for the rest of my sample and produce denoised data. I’ve followed the documentation as best as I can but I’m getting an error I can’t figure out.
Each of the filtered_func_data.ica directories listed contains (among other things) a melodic_IC.nii.gz file and a hand_labels_noise.txt file which has as it’s last line a bracketed list of all component numbers for that subject which I classified as noise. The output of this command was as follows repeated for each of the 10 training subjects. Can someone please explain what I’m doing wrong?
Command used (and if a helper script was used, a link to the helper script or the command generated):
/usr/local/fsl/fix/fix -t /bcdlab/CoAPilot/NBack.Rdata /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1020/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1021/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1022/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1023/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1024/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1025/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1026/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1027/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/ /bcdlab/CoAPilot/1028/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/
copy true labels and features into training directory
FIX features not already generated, so creating them now.
FIX Feature extraction for Melodic output directory: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica/
create edge masks
run FAST
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
terminate called after throwing an instance of 'std::runtime_error'
what(): Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
/usr/local/fsl/fix/fix_0b_apply_fast: line 11: 99597 Aborted (core dumped) fast -t 1 -o ${folders}/fix/fastsg ${folders}/reg/highres
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
registration of standard space masks
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/highres
Could not open matrix file /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//fix/highres2std.mat
Cannot read input-matrix
Could not open matrix file /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//fix/std2highres.mat
Cannot read input-matrix
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #63 :: No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Image Exception : #22 :: Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Failed to read volume /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
Error : No image files match: /bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//reg/example_func
extract features
Unable to find MATLAB Compiler Runtime
/usr/local/fsl/fix/call_matlab.sh [-z <mode>] [-o <options>] [-p <path>] [-h <fix path>]
[-c <mcr path>] [-b <binaries path>] [-l <logfile>]
{-r <"MATLAB code">|-m <script>|-f <function> [arguments...]}
-z <mode>: This overrides the environment variable
FSL_FIX_MATLAB_MODE which would otherwise control this.
0 = Use compiled MATLAB function specified by
-m <function name>
1 = Use MATLAB - requires -r or -m option
2 = Use Octave - requires -r or -m option
-r <"MATLAB code">: Evaluate the double-quoted MATLAB/Octave
code. Equivalent to 'matlab -r "MATLAB code"' or
'octave --eval "MATLAB code"'
Ensure that any double quotes in this string are escaped
with '\'.
-m <script>:
-z = 0 or not provided, run as -z = 1
-z = 1|2 - Run <script> in MATLAB/Octave
Equivalent to 'matlab \< <script>.m' or 'octave <script>.m'
-f <function> [arguments]:
-z = 0 - Call compiled MATLAB <function>
Arguments to be passed are given in the remainder of the
command line.
-z = 1|2 - Run <function> script in MATLAB/Octave
Equivalent to 'matlab -r "<function>([arguments])"' or
'octave --eval "<function>([arguments])"'
Arguments to be passed are given in the remainder of the
command line.
-o <options>: Double quoted list of MATLAB/Octave command line
options. Defaults to ${FSL_FIX_MLOPTS} or ${FSL_FIX_OCOPTS}
respectively
-p <path>: Path to MATLAB/Octave startup script/binary.
Defaults to: ${FSL_FIX_MATLAB} or ${FSL_FIX_OCTAVE}
respectively
-h <path>: Path to folder containing the Fix programs
-w <path>: Path to FSL MATLAB helper functions, defaults to
/usr/local/fsl/etc/matlab
-c <mcr path>: Path to MATLAB Compiler Runtime for the version
of MATLAB Fix was compiled under. Defaults to ${FSL_FIX_MCR}
-b <compiled path>: Path to the folder containing the compiled MATLAB
functions. Defaults to ${FSL_FIX_MLCDIR}
-l <logfile>: Append console and error output to <logfile>\n
cp: cannot stat ‘/bcdlab/CoAPilot/1019/V1/Data/NBackPreproc.feat/filtered_func_data_Dissertation.ica/filtered_func_data.ica//fix/features.csv’: No such file or directory
Version:
FIX (FMRIB’s ICA-based Xnoiseifier) v1.06.15
Environment (Docker, Singularity / Apptainer, custom installation):
Red HAT Linux Version 7.9 (Maipo) 64bit
Data formatted according to a validatable standard? Please provide the output of the validator: