Hi Raimon,
Following up on this thread:
Running the bet command listed in the manual on example_func for each participant yielded two masks: one binarized, one non-binarized. Do I use the binarized mask when running ICA-AROMA in the case of linear registration?
Separate from this thread:
For nuisance regression, I have segmented CSF and white matter (WM). These maps will be registered to native space, then I will extract time series for each to regress from the ICA-AROMA "denoised_func_data_nonaggr.nii.gz", apply high-pass filtering, and finally, register the finalized "denoised_func" to MNI space. (I gathered the various steps/details from previous threads.)
**If I applied linear registration, I assume I would be using flirt/applyxfm, whereas if I used nonlinear registration, I would be using fnirt/applywarp to register "denoised_func" to MNI space?
Thank you for your assistance!
Cheers,
Erin
Dear Frederik,
The current version of ICA-AROMA indeed assumes that you ran non-linear registration when using the Feat-option ('-feat').
However, it is possible to run ICA-AROMA with only your affine registration file (to MNI152). Then you need to run ICA-AROMA in the generic manner (see section 4 of the manual), without the '-feat' option, and simply don't specify the '-warp' but only the '-affmat' argument. Preferably you derive a mask as explained in section 4.1.
For an example how to run ICA-AROMA in this case, check section 7.3 of the manual.
FYI: The registration files will only be used to register the components to the MNI-template in order to derive spatial feature scores using the provided (standardized) edge & csf masks. The quality of the registration should therefore be such that these masks are appropriate. To that end, the affine registration will probably do most of the job to accommodate this.
Best,
Raimon
-----Original Message-----
From: FSL - FMRIB's Software Library [mailto:[log in to unmask]] On Behalf Of Frederik Bartels
Sent: woensdag 13 mei 2015 10:36
To: [log in to unmask]
Subject: [FSL] ICA-AROMA after Feat
Hi,
I want to run ICA-AROMA after FEAT. When I run it with the Feat input it gives me this error:
"Missing reg/highres2standard_warp.nii.gz in Feat directory."
I ran Feat with affine registration (FLIRT). Do I need to run nonlinear registration (FNIRT) in Feat in order to use ICA-AROMA? Or where and how do I get my warp file?
Thank you for your help!
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