Select my pipeline with FALFF

[Moyan Li]

Hi,

I have a question when I follow the instructions on the website to select my pipeline. The raw data for each subject is a 4D time series data with dimension 91*109*91*1200, where 1200 represent that we collect the image at different 1200 time. Now I want to make each subject's data into a 91*109*91 image. I plan to use fractional amplitude of low frequency fluctuations(falff) pipeline. I found a template pipeline.yml file here https://github.com/FCP-INDI/C-PAC/blob/master/dev/docker_data/default_pipeline.yml 

If I only want to use falff to preprocssing the data, does that mean I only need to set the part below as "On":

amplitude_low_frequency_fluctuation:
# ALFF & f/ALFF
# Calculate Amplitude of Low Frequency Fluctuations (ALFF) and and fractional ALFF (f/ALFF) for all voxels.
run: On
# Frequency cutoff (in Hz) for the high-pass filter used when calculating f/ALFF.
highpass_cutoff: [0.01]
# Frequency cutoff (in Hz) for the low-pass filter used when calculating f/ALFF
lowpass_cutoff: [0.1]

I am not sure if there is any other things I need to do to finish that pipeline.yml file. I also tried to use https://fcp-indi.github.io/C-PAC_GUI/#/, but I dod not find the falff option to propress my data.

Thanks in advance for your help!

best,

Moyan

[sgia...@gmail.com]

Hello Moyan,

Enabling only ALFF + f/ALFF will send the raw BOLD data directly into the calculation of those measures.

Note ALFF and f/ALFF are considered final outputs/derivatives, and is not a form of preprocessing.

The functional preprocessing part of the pipeline is what preprocesses the data, and nuisance correction "cleans" it.

Please let me know if you have any further questions.

Best,

Steve

[Moyan Li]

Hi Steve,

Thanks for your explanation. I see your point. I am wondering if I could just get ALFF and f/ALFF derivatives without doing any preprocessing using C-PAC.

Best,

Moyan