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, andrewkra...@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 <ni...@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, andrewkra...@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 > >> > >> > > > > _______________________________________________ > > 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. > > > > > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
