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:
External Email - Use Caution
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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