Hi Freesurfer
I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic?
When I ran recon-all on the 1mm atlas it created some nice surfaces.
Let me know if you would like the .log as I cannot seem to make much sense of it.
best wishes
Trisanna
-- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
Hi Trisanna,
you can find instructions on how to process data with an isotropic resolution other than 1mm^3 with FreeSurfer v5.1 and above here: https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon
For v5.3 the pipeline should be slightly adapted, however, can easily be done. If you need assistance, just let me know. In the upcoming release of v6 this workaround will not necessary anymore.
Best, Falk
Von: freesurfer-bounces@nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] Im Auftrag von Trisanna Sprung-Much Gesendet: Mittwoch, 25. Mai 2016 17:35 An: Freesurfer support list Betreff: [Freesurfer] recon-all on 0.5mm scan?
Hi Freesurfer I would like to know if it is possible to create surfaces from a scan that is 0.5mm isotropic. I tried to run recon-all on our MNI 2009b atlas which is 0.5mm cubed and it crashed quite quickly afterwards. I wonder if this has to do with the fact that Freesurfer tried to conform it to 1mm isotropic? When I ran recon-all on the 1mm atlas it created some nice surfaces. Let me know if you would like the .log as I cannot seem to make much sense of it. best wishes Trisanna -- Ph.D. Candidate McGill University Integrated Program in Neuroscience Psychology
freesurfer@nmr.mgh.harvard.edu
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Falk Lüsebrink -
Trisanna Sprung-Much