ROI analyses with fslmeants and featquery not working with fMRIPrep data due to different sizes

[Jacob_Elder]

Hi,

I am trying to run ROI analyses in FSL, but when I try to run to run Featquery, I get the error, “Error - mask size doesn’t match any of the images in the FEAT directory” and when I run fslmeants, I get, “Mask and Input volumes have different (x,y,z) size.”

I used Jeannette Mumford’s Feat workaround in order to use FSL with fMRIPrep output.

I encountered the following two resources, which were helpful but did not fully resolve my issue:

Extract ROIs from fmriprep output epi bold images

Hi, i have preprocessed my resting state data using fmriprep. If I understand it rightly, bold images are co-rerigstered to MNI152NLin2009cAsym template. Now, I want to extract some ROIs. Are there any atlases avaliable in this space? I have tried to use AAL2 atlas, but ROI-masks and bold images do not match. Does anybody have any ideas how to solve this problem? Thank you! Cheers, Dima

FSL featquery with fmriprep'd data

Hi again, It seems that featquery fails because the highres2example_func.mat file does not exist after deleting reg/*.mat in the registration workaround. The registration work around only creates the example_func2standard.mat How do I address this issue? I am not sure how to create the highres2example_func.mat Thank you in advance

The updatefeatreg resolution described in second link works if you want to run featquery on your first-level. But I have three levels-- Runs then subjects then group. So updatefeatreg will not run for my second level.

As described by Chris in the first link, “The voxel size or FOV do not match (because FMRIPREP uses the resolution of the input images), but the locations should overlap nicely when you open the data and the atlas in Mango or FSLeyes.” My voxel size is in fact different from the mask, but they do line up well with the binarized atlas mask. But fslmeants and featquery still will not accept the mask for my fMRIPrep images.

I’m pretty stumped here. Should I warp my data to MNI_2mm? That seems unnecessary and not like the right thing to do, right?

[Jacob_Elder]

I got an ROI to work in fslmeants by following the instructions described here of resampling the mask to the the fMRIPrep MNI152NLin2009cAsym space. Featquery still returns an error though, even with the resampled mask.

Is this the best way to get atlas structures to work with fMRIPrep output?

How to transform mask from MNI to native space using fmriprep outputs?

I have a mask of visual cortex created in MNI space. I pre-processed my fMRI data with fmriprep. Now I want to get my mask from MNI to native (functional BOLD) space. How can I make use of the fmriprep outputs to achieve this? Previously, I combined the inverse of the co-registration from anatomical to MNI space and the inverted transformation matrices of the co-registration from functional to anatomical space using FSL’s applywarp. Thanks in advance for your help and please let me know if you n…

[Dmitriy_Desser]

Have you already tried this:

Extract ROIs from fmriprep output epi bold images

I just wanted to mention two developments regarding this issue: fMRIPrep now allows you to generate derivatives exactly matching templates other than MNI152NLin2009cAsym. That is using the new --output-spaces argument. For instance: --output-spaces MNI152NLin6Asym:res-2 will give you preprocessed fMRI with the grid of the FSL MNI template (i.e., 2mm isotropic resolution and 91x109x91 matrix size). TemplateFlow now includes the harvard-oxford template resampled to the default template of fM…

Best,

Dima

[Jacob_Elder]

Ah, I missed that. I will re-run preprocessing with fMRIPrep with that option set. Thank you.