mri_convert --help has info on specifying orientation, with suitable warnings about the need for you to make sure you know which way is correct.

n.

On Wed, 2011-02-23 at 14:55 -0800, andrewkrause@ucla.edu wrote:

Thanks for the reply. For the orientation, I know from working with the sources of the average that it's in neurological (left = left) orientation. Is there a way to let mri_convert know this (it looks like ANALYZE is usually radiological so I don't know if this is what is assumed)? Unfortunately I don't know if it's possible to make the average in nifti format instead, since everything is currently set up using ANALYZE (i.e. the scans it's averaging are already in ANALYZE).

-- Andrew

Quoting Nick Schmansky nicks@nmr.mgh.harvard.edu:

...

add the flag -notal-check to the end of recon-all command to skip the check.

if you can make your average using nifti format you're better off as analyze doesnt retain orientation (l/r) info.

you may have to manually register the brain following this: http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach

n.

On Wed, 2011-02-23 at 13:38 -0800, andrewkrause@ucla.edu wrote:

...

Hello,

I'm a complete newbie to FreeSurfer, so I appreciate any and all help you can provide. I am trying to use FreeSurfer to automatically create some masks of subcortical structures, but am having trouble getting the whole process started.

When I run "recon-all -autorecon1 -noskullstrip -s FAD" (where FAD is my subject name) it quits with the error

"ERROR: talairach_afd: Talairach Transform: transforms/talairach.xfm ***FAILED*** (p=0.0000, pval=0.0000 < threshold=0.0050)"

I am trying to do this to a skull-stripped brain originally in Analyze format (there are no DICOMs since it's actually an average of many skull-stripped scans), to which I've already registered all of the scans I want to study. I used mri_convert to convert the .img file into a .mgz file, but compared to the bert example, the background (non-brain area) is a light gray instead of black. I don't know if this is where the error is occuring, and if it is, how to correct it. If it helps, the scan I'm trying to create masks from has been registered to the ICBM brain template.

Let me know what other information you need and thanks for the help, -- Andrew _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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