Hi Falk,

Thanks for this valuable information.  For sure, I will try it out, and let you know how it goes. 

Xiaomin

From: falk.luese@gmx.net
To: freesurfer@nmr.mgh.harvard.edu
Date: Thu, 3 Apr 2014 00:32:23 +0000
Subject: Re: [Freesurfer] recon all with 7T data

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: ýMittwochý, ý2ý. ýAprilý ý2014 ý15ý:ý23
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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_______________________________________________ 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.