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Hi Mark, Thank so much for your response. I tried the following: flirt -in voxel_overlay_GM_LP200.nii -ref c1T1MEMPRAGEs005a1001.nii (gray matter mask in native space) -out LP200_GM_rACC.nii -omat invol2refvol.mat -dof 6 This did not work at all. I got a warning message WARNING::in calculating COG, total = 0.0. I wonder if it would be helpful to show you the gray matter brain with rACC mask. Would you be willing to take a look? Could I send it to you via a private email rather than the mass FSL list? Is it an issue that it is not binarized, that is it contains 0s, 1s, and 2s? Thanks!!! Emily ________________________________ From: FSL - FMRIB's Software Library <[log in to unmask]> on behalf of Mark Jenkinson <[log in to unmask]> Sent: Wednesday, March 1, 2017 5:32:46 PM To: [log in to unmask] Subject: Re: [FSL] Registering Gray Matter Mask back to T1 Hi, You could try to register the gray matter mask to a gray matter mask in native space and then threshold the transformed version. A combination of fslmaths and flirt should be good enough to do this. I don't really know what the SPM options are though, so for those options you'd need to ask the SPM list. All the best, Mark On 27 Feb 2017, at 19:53, Emily Louise Belleau <[log in to unmask]<mailto:[log in to unmask]>> wrote: Hello FSL Experts, I am working on combining MRS with resting state connectivity. I am trying to use the MRS voxel as the seed for the resting state connectivity. For each subject, our physicist gave me the MRS voxel (rostral anterior cingulate cortex) overlayed onto each subject's gray matter mask. However, the physicist did a lot reorienting/resizing of the gray matter mask to fit the MRS voxel in FSL, so that the gray matter mask is no longer in native T1 space. I would like to get the gray matter mask with the overlayed MRS voxel back into T1 space. Since I ultimately preprocessed the resting state data in SPM, I planned to warp the rACC mask using SPM normalization since I know that SPM MNI space is a bit different from FSL MNI space. Any thoughts on how best to go about doing this? The racc_mask overlay is labeled a "2", all the gray matter is labeled a "1", and everything else is labeled "0". Thanks you! I sure would appreciate any guidance! Emily