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: j...@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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it is > addressed. If you believe this e-mail was sent to you in error and the e-mail > contains patient information, please contact the Partners Compliance HelpLine > at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. >
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