Yes, this is a bug. I have fixed it in our development version. For now, you can use your workaround.
On 12/7/2024 1:28 AM, Shen, Qian wrote:
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Hi Dr. Greve and Experts, I encountered an issue while running the following command to resample meltzer.nii.gz (or mgx.subctxgm.nii.gz) into the 2mm MNI305 space, as instructed in the PetSurfer wiki https://secure-web.cisco.com/1W31n5cbq1zvsFiHcecMWmqEEiH13OUvfTH7j9X72O1GdvrVgS254whgv2ZAx19Ru0yqKh99ubP7fx3Dui23TsH2W0i6TBUkShiy1siHUzcyj0-5173p6Eh_UThR_xYiaeP7g8eTh_W_llC-IfUY1p6GKv6qfDnDJitLLnjRBDopfe-9hfaFXnWr5BDGc_P8fm2rBmpmGWfJA6ZcLv3AZY5zwwNxaXaxWFn7wusLjWtT4D93i4q-6lHaieMZLAIZNOoMveWB2dUQhWBe1idjbOIb84oJNIkHkfCgF1xBPirVVC-btdA7n6l8wE0aqGS6ugdAUD5dnJeYG8p9BTqWTFg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FPetSurfer. The output image appeared misoriented (see the attached screenshot for reference): mri_vol2vol --mov meltzer.nii.gz--reg aux/bbpet2anat.lta --tal --talres 2 --o meltzer.mni305.2mm.sm00.nii.gz Upon investigating, I realized the issue arises when using the --no-reduce-fov option in the mri_gtmpvc step. Specifically: (1)If I do not use --no-reduce-fov in mri_gtmpvc, the output image from above mri_vol2vol command is correct. (2)Alternatively, if I do use --no-reduce-fov, but replace aux/bbpet2anat.lta with either template.reg.lta or aux/anat2bbpet.lta in mri_vol2vol command, the output image is also correct. Could you confirm if this behavior is expected or if additional adjustments are needed? By the way, the version of Freesurfer I'm using is v7.1.0. Thank you for your guidance in advance, Shen
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