Hi Noelle,
If you want to restore FreeSurfer-space images to the original space then try the following (as it has worked for me in the past but I cannot guarantee it):
flirt -in freesurfer_space_image -ref original_space_image -usesqform -applyxfm -out reorientedFSimage
Hopefully the output will then be the FreeSurfer image you wanted (e.g. the brain extracted image or brain mask) in the original space.
All the best,
Mark
From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Noelle Dalin <[log in to unmask]>
Reply-To: FSL - FMRIB's Software Library <[log in to unmask]>
Date: Wednesday, 24 August 2016 at 00:36
To: "[log in to unmask]" <[log in to unmask]>
Subject: [FSL] Using Freesurfer for skull stripping/ brain extraction then reorienting images to use in FSL
Hello all,
BACKGROUND: My lab is working with paediatric brain images with lots of motion. We have been playing around with the settings of BET (command line) and then manually editing the masks using the eraser and pencil tools. However, we have found that this is an extremely long process taking hours and hours to get the images to turn out well.
We also have tried using freesurfer for the skull stripping and it takes about an eighth of the amount of time to get an even better brain image. So we want to use freesurfer to get out brain only images moving forward. The problem is that, in freesurfer, the images are in a different orientation than those in FSL. For example, the same brain extracted image in freesurfer seems to be rotated a bit more to the left than the image extracted in FSL.
QUESTION: Does anyone with freesurfer or FSL knowledge know how to convert the freesurfer’s brain-only images so that we can use them in FSL for ICA (both group and individual) as well as TBSS and Tractography( back on freesurfer)?
Thank you for your time and expertise.
Cheers,
Noelle Dalin
