Error running ICA-AROMA #51
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Hi Stephan, |
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Thanks a lot for your reply. That error looks different: ------------------------------- RUNNING ICA-AROMA ------------------------------- Step 1) MELODIC
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yes: "Found 20 head motion-related components in a total of 20 components." i.e., all of your components are marked to be removed from the data, nothing would be left... Something is likely off, either in your data itself (e.g., a severe artifact) or in the analysis path (e.g., registration failed so your brain data is not on the standard brain) |
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or because I set the criteria to -dim 20? |
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potentially, but unlikely. A good indication could be to see how many components melodic returns if you don't set the dimensionality to 20. Is there a particular reason why you did this? We typically recommend to not set the dimensionality for denoising purposes (unless you have a huge number of volumes e.g., in the case of multiband data). |
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without the command it works: ------------------------------- RUNNING ICA-AROMA ------------------------------- Step 1) MELODIC
----------------------------------- Finished ----------------------------------- |
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But I am still having the error from above: --------------- 'ICA-based Automatic Removal Of Motion Artifacts' --------------- Step 1) MELODIC and it is not a memory error. |
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This error is related to FSL's melodic and not ICA-AROMA. I suspect something is off with your input data or the mask that is being calculated. Have you looked at the raw data? Have you tried running melodic directly on those data? |
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The input data looks fine. And running directly with melodic works. |
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Do the components look sensible? You can now also try to run AROMA where you provide the melodic directory you just created. If you run melodic as part of FEAT, AROMA will detect the .ica directory and not rerun melodic. |
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How would I provide the output directory to AROMA? for ((i = 1; i < 2; i++));for ((ses = 1; ses < 8; ses++)); sub-1_ses-1_task-rest_run-3_space-MNI152NLin2009cAsym_desc-preproc_bold_skipped_5_smoothed_6.ica is the created output directory. |
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use the -md option. The -out option is for the directory where you want AROMA to save its results... python2.7 /Users/neurolab/Desktop/Stephan/Programmes/ICA-AROMA-master/ICA_AROMA.py --help gives your more info... |
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ah, great. Could not find that command in the manual. What would be your thoughts on that? |
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running ICA-AROMA after melodic gives the following error: ------------------------------- RUNNING ICA-AROMA ------------------------------- Step 1) MELODIC
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something is off either with your registration parameters or with the mixture modelling thresholding. Did you run melodic with the --Oalll and the --Ostats option? |
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Yes, I tried that as well. The registration looks fine of the functional bold image. |
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based on this: "The MELODIC directory does not contain the required 'stats' folder. Mixture modeling on the Z-statistical maps will be run." it looks like you're not providing the melodic run with the --Oall or the --Ostats option? |
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With that option it changed to: ------------------------------- RUNNING ICA-AROMA ------------------------------- Step 1) MELODIC
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is there a way for you to send me a copy of this data? Preferably the preprocessed data with everything tarred up into a single archive. |
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I could post screenshots if that would help? |
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no, I would want to take a look and run a couple of things myself. If you can host on dropbox or something alike - password protected. Shoot me an email on m dot mennes at donders dot ru dot nl |
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did u receive it? |
Dear all,
I ran ICA-AROMA for several subjects and everything worked well.
For some subjects I encounter the following error, although they are very similar to the ones where ICA-AROMA works fine:
------------------------------- RUNNING ICA-AROMA -------------------------------
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------
Step 1) MELODIC
libc++abi.dylib: terminating with uncaught exception of type std::logic_error: subtraction: incompatible matrix dimensions: 0x0 and 1x0
Traceback (most recent call last):
File "/Users/neurolab/Desktop/Stephan/Programmes/ICA-AROMA-master/ICA_AROMA.py", line 204, in
aromafunc.runICA(fslDir, inFile, outDir, melDir, mask, dim, TR)
File "/Users/neurolab/Desktop/Stephan/Programmes/ICA-AROMA-master/ICA_AROMA_functions.py", line 94, in runICA
nrICs = int(float(subprocess.getoutput(cmd)))
ValueError: could not convert string to float: Image Exception : #63 :: No image files match: /Users/neurolab/Desktop/Drmed/CART_Code_rearranged_concat_prep/derivatives/participant/fmriprep/sub-10/ses-5/func/ICA_AROMA/melodic.ica/melodic_IC
No ima
I couldn't find out why this is happening,
Best,
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