Hi Talia,
		 Yes - if you have a "template" design.fsf with fieldmaps set, you need to modify the keys pointing to the fieldmap inputs.
Kind Regards
Matthew
> Hi Matthew,
> I see. The idea about using a design.fsf is what I thought based on searching around. I was partly hoping there would potentially be some command line options that I would pull from FEAT since MELODIC does FEAT preprocessing. I was basing this idea from looking at the report log and seeing they have different options to set the parameters for preprocessing and registration. However, thinking about that, I realize it probably would be more tedious than a design file and have the script input the different subjects. 
> These command such as set fmri and set feat_files(1) would be the same if I were to input a fieldmap to unwarp the EPI correct? it would set fieldmap and set fieldmap_mag.
> Thank you for your help!
> Best,
> Talia
> ________________________________________
> From: FSL - FMRIB's Software Library [[log in to unmask]] on behalf of Matthew Webster [[log in to unmask]]
> Sent: Friday, April 29, 2016 11:45 AM
> To: [log in to unmask]
> Subject: Re: [FSL] Scripting with MELODIC ICA
> 
> Hello,
>           The command line melodic does not perform _any_ preprocessing - this is all done by scripts that are called by the GUI. If you are happy with the default melodic behaviour, then you can script GUI-like behaviour by setting up the GUI for one input file, and save the design.fsf. The design.fsf can then be modified for other inputs - minimally the values of the input and output files need to be changed, these values are defined by the following keyed entries in the design.fsf
> 
> set fmri(outputdir) "/path/to/dir"
> set feat_files(1) "/path/to/file"
> 
> this fsf can then be run, by passing it to the feat script ( this script handles both FEAT and MELODIC generated fsfs )
> 
> $FSLDIR/bin/feat design.fsf
> 
> Hope this helps,
> Kind Regards
> Matthew
> 
> 
>> 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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