Results not aligning well with MNI space after 3dlme

Hi everyone,

My first level data has been co-registered to the standard MNI space (MNI_T1_2mm) and loads fine in MRIcroGL and FSLeyes. However, after running the 3dlme command, my result file no longer aligns well with the MNI space. Could you please help me understand what I might be doing wrong? I’m attaching the images to illustrate the problem.

Thank you in advance,


What is the output of “3dinfo -obliquity DSET” on the dset that you put into 3dLME?

And I guess what is the output of this command:

nifti_tool -disp_hdr -infiles DSET


I ran the commands you recommended on a sample file:

3dinfo -obliquity Common_tb5388_stress_bis_AvgMiddle2RunsREML_sm6_orig_mask_RAS.nii.gz

Output: 0.00

nifti_tool -disp_hdr -infiles Common_tb5388_stress_bis_AvgMiddle2RunsREML_sm6_orig_mask_RAS.nii.gz

Output: please see the attached image for the full output.

I’ve also ran the nifti_tool command on the output from the 3dlme and I’m attaching that as well.

p.s. Also happy to email the two files directly if that would be helpful.