maartenmennes/ICA-AROMA

Components are classified, but no denoising.

Santoucha opened this issue · 5 comments

Santoucha commented

Hi,

I'm running ICA-AROMA on .feat directory with command:
python3 ICA_AROMA.py -feat data.feat -out data.feat/ICA_AROMA/

The pipeline works fine, until at the data denoising. It classifies noise and makes a classified_motion_ICs.txt file, but it says that none of the components were classified as motion...

Here is the log:

------------------------------- RUNNING ICA-AROMA -------------------------------
--------------- 'ICA-based Automatic Removal Of Motion Artifacts' ---------------

Step 1) MELODIC
Step 2) Automatic classification of the components

  • registering the spatial maps to MNI
  • extracting the CSF & Edge fraction features
  • extracting the Maximum RP correlation feature
  • extracting the High-frequency content feature
  • classification
    Step 3) Data denoising
  • None of the components was classified as motion, so no denoising is applied (a symbolic link to the input file will be created).
    Traceback (most recent call last):

File "/../ICA_AROMA.py", line 215, in
aromafunc.denoising(fslDir, inFile, outDir, melmix, denType, motionICs)
File "/../ICA_AROMA_functions.py", line 558, in denoising
os.symlink(inFile,os.path.join(outDir,'denoised_func_data_nonaggr.nii.gz'))
FileExistsError: [Errno 17] File exists: '/..//filtered_func_data.nii.gz' -> '/../denoised_func_data_nonaggr.nii.gz'

I'm wondering if you have a solution for this problem?

I attached the classified noise files as attachment.
classified_motion_ICs.txt
classification_overview.txt

Hope to hear from you soon.

Kind regards,
Santoucha

maartenmennes commented

Hi Santoucha,

not sure what the problem is, but the error message you are receiving suggests that you might have run AROMA a second time on the same dataset? i.e., it indicates that denoised_func_data_nonaggr.nii.gz already exists. I'm guessing that is why it's also indicating that no components were labelled as noise.

Would that be a possibility?

What is the timestamp of the different files in your folder?

Santoucha commented

Hi Maarten,

Thanks for reply.
I only ran AROMA once on the same dataset and tested it on more than one dataset. Each time it gives me the same error.
The timestamps of my ICA-AROMA folder:
classification_overview.txt 17:24
classified_motion_ICs.txt 17:24
denoised_func_nonagrr.nii.gz 17:24
feature_scores.txt 17:24
mask.nii.gz 17:14
melodic_IC_thr_MNI2mm.nii.gz 17:19
melodic_IC_thr.nii.gz 17:19
melodic.ica directory 17:14.

It looks like the step of checking the classified_motion_ICs.txt file goes wrong, so it makes a symbolic link from my filtered_func_data.nii.gz file (in my feat folder) and renames it denoised_func_data_nonagrr.nii.gz.
I can't attach the python that I'm using but, I checked it, and it seems as it is the latest version.

Thanks for looking in to this!

Kind regards,
Santoucha

maartenmennes commented

Can you try with the version I updated today, as this might be related to the indentation issues...

Santoucha commented

Yes, it works just fine now! Thanks a lot for looking into this!

Kind regards,
Santoucha

maartenmennes commented

Excellent!