Hi Steven,

It has been recommended to me that in case of Tal-check failures, the use of the -use-mritotal flag will overcome this issue. However, this substitutes Freesurfer's registration algorithms with a function from MNI, I believe. In general, I have heard it said that mritotal does a poorer job, than the freesurfer implementation, thus this may not be the best option.

In the current version of Freesurfer, as I have been told, talairach.xfm is needed to compute nu.mgz, [and] talairach stage needs to precede the nu_correct stage. In my data set, this has led to poorer registration, and hippocampal segmentations.

At first, I resolved to use mritotal which helped things somewhat. However, on a recent thread on the list-serve, a modified recon-all script file was posted by Nick Schmansky that resolves this issue. In the script are some changes that will be put into the next version release of Freesurfer, one of which resolves the talairach issue. I downloaded the script, and replaced the 5.1 version of the recon-all script. You will find the recon-all script in a message entitled:

[Freesurfer] How to switch order of Talairach and nu-correction stages in recon-all

As I mentioned, this new recon-all file resolved my issue with poor hippocampal segmentations

- Joshua Lee

On Thu, Apr 19, 2012 at 8:51 AM, Steven Korycinski stvkory@umich.edu wrote:

Hi all,

I've been following an e-mail on this list-serve from Joshua Lee regarding poor hippocampal segmentations in Freesurfer 5.1. He mentions "using -use-mritotal in the recon-all command to overcome tal-check failures" to help fix the segmentation and make them more like "those produced by Freesurfer version 4.xx." In light of this information, would you recommend that all normal Freesurfer 5.1 users add this flag to the recon-all command to help with any segmentation errors? Also, at what stage(s) in the reconstruction process should the flag be included (ie. recon-all -autorecon1,2, or 3)?

Thanks,

Steve _______________________________________________ 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.