Hi Xiaomin,
you could also try to follow the first few steps of the HiresRecon (http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). The parameters of the inhomogeneity correction are optimized for 7T data which should help in reducing errors due to strong bias fields.
Best,
Falk
Von: Xiaomin Yue Gesendet: Mittwoch, 2. April 2014 15:23 An: Freesurfer support list
Hi Joe,
Thanks for your response. For the future reference, it also needs the parameter -notal-check, otherwise it will fail again. Although the reconstruction was completed surprisingly without error, a significant amount of cortex in the top of the brain was cut off in the brain.mgz file. It needs to be rerun after correcting that error(s).
Xiaomin
Date: Tue, 1 Apr 2014 19:52:53 -0400 From: jonp@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon all with 7T data
hi Xiaomin,
7T data can sometimes cause Talairach failures with the standard registration tools due to the strong bias fields. the Talairach transformation is used for identifying seed points, and the -use-mritotal flag just specifies that the MINC software will be used for the Talairach'ing.
see this page for more info: http://freesurfer.net/fswiki/talairach?highlight=%28use%5C-mritotal%29
-jon
On Fri, 28 Mar 2014, Xiaomin Yue wrote:
I tried to do surfer reconstruction (version 5.3) collected in SIEMENS 7T, with error: imgreg_4dfp /opt/freesurfer-530/average/711-2C_as_mni_average_305 /opt/freesurfer-530/average/711-2B_as_mni_average_305_mask talsrcimg_g11 none talsrcimg_to_711-2C_as_mni_average_305_t4 1283' failed! status=254. This seems happened for many others. However, the reconstruction worked fine as using data collected from 3T, which means the freesurfer was installed correct, and environment settings are correct as well. Also, the reconstruction on the 7T data can go through using additional parameter: -use-mritotal. My question is how the -use-mritotal parameter would affect final surface? Thanks for providing your input on this. Xiaomin Yue
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