Fmriprep downsamples MRI images

Dear all,
when I compare my original mri image with the output mri image from fmriprep the amount of voxels have decreased. Is there a way to avoid a great drop image resolution (amount of voxel)?

Best,
Steph

Could you give a little more detail about your original files, or the fMRIPrep command you’re using ?

By default, fMRIPrep should be keeping the original resolution of the BOLD data to produce smaller files, more consistent with the original data gridding. If you’d like it to resample BOLD files to, say, the 2mm isotropic resolution of the MNI152NLin2009cAsym template, there’s a bit more detail on how to do so here.

1 Like

So thats my command:

for ((i = 52; i < 100; i++)); fmriprep-docker /Users/neurolab/Desktop/Test_GSP_final /Users/neurolab/Desktop/Test_GSP_final/derivatives/participant --participant-label $i --fs-license-file /Users/neurolab/Desktop/Stephan/Programmes/freesurfer/license.txt --fs-subjects-dir /Users/neurolab/Desktop/Test_GSP_final/derivatives/freesurfer/sub-$i

My original mri images are of dimension 91,109,91 and the outputs (sub-10_ses-1_task-rest_run-1_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz) are 65,77,65.
When I add —use-aroma the dimension stay the same.
Best

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