Hi all,
I'm trying to do an ICA on some resting state data that I have. I'm a beginner at FSL. I originally was doing seed-based connectivity in FreeSurfer and unpacked the resting state data with dcmunpack. This is relevant as I used the nifti files as the input data for the MELODIC toolbox. I want to figure out a way how to automate this process. On the FSL wiki though, it says " Note, therefore that the melodic command-line program will not do the preprocessing for you that the GUI-based scripting will do. The GUI will allow you to change some of the most common default options for the preprocessing and the basic options for the final ICA decomposition. To get full control over the latter, use the command line version melodic --help" It seems that melodic --help doesn't include all the options for setting up specific settings for preprocessing. This information is a bit confusing to me because I'm not sure what they mean by GUI-based scripting. Would you have to create a .fsf file?
I first attempted to simply run the command line melodic -i f.nii.gz -o subj.ica --tr=5.000 etc etc. and have it do the ICA with most of its default settings to see how the results turn out. However, the issue comes during registration. It says it can't find example_func2standard.mat. I understand that it's informative and that the program generates its own transform but if I wanted to try doing FLIRT/FNIRT separately to create this .mat file, how would the program know to register that as an input? Also, when I try to register a structural image nifti file as the main structural image, it runs into an error. My input for the main structural image is a brain.nii.gz that FreeSurfer created after dcmunpack/preprocessing.
So my question is how do I implement other preprocessing options or post-stats options that I want to use for MELODIC. I'm thinking that maybe I should use FEAT instead and turn on MELODIC ICA data exploration? What is the best approach?
Thank you!
Best,
Talia
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