External Email - Use Caution Dear Vale,
using the GUI of SPM you cannot get a FWHM of lower than 30. You have to save the batch to disk, load it in MATLAB and change the parameters to your liking. In case this sounds too complicated, you can use part of a reconstruction pipeline I have put together on Github. Just get the files from this folder: https://github.com/fluese/reconstructionPipeline/tree/master/processingPipeline/biasCorrection To use it: SPM12 needs to be properly set up (e.g. added to MATLAB path), change the variables to your liking (either by creating a settings variable with the given structure or just hardcode it in the m-file), the variable filename should contain the path as well if the script is run from a different folder than the data is located at. I haven't worked with MEMPRAGE data myself, so somebody else may chime in on that. However, the echoes should simply be combined by RMS (https://surfer.nmr.mgh.harvard.edu/fswiki/UserContributions/FAQ#Q.Isitrecommendedthatpeopleusememprage.3FHowaretheyanalyzed.3FJustsqrtsumsqroftheechoes.3FOristheresomethingmoreelaborate.3F) and can for example be done using mri_concat (https://surfer.nmr.mgh.harvard.edu/fswiki/mri_concat?highlight=%28memprage%29). Although I remember vaguely, that the combination of echoes was implemented somewhere else as well. In case you have further questions, just let me know. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Barletta, Valeria Gesendet: Mittwoch, 19. Februar 2020 17:19 An: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Betreff: [Freesurfer] bias correction on 7T MEMPRAGE Dear Freesurfers, I am trying to apply the bias correction on the 7T MEMPRAGE through the unified segmentation algorithm on SPM12, as a primary step to do the submillimetric recon on Freesurfer, as you suggested here: https://surfer.nmr.mgh.harvard.edu/fswiki/HighFieldRecon For some reason, I cannot set the Bias FWHM to 18 on the SPM12 interface. Also, not sure how to use the 5D image that I obtain from the process. Have you ever done this before? Any tips? Thanks a lot, Vale
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
