Hi Jeff,
it's hard to sort out what happened as it looks like you invoked recon-all over 50 times for this subject! In any case, the talairach.lta was way, way off, but when I just reran mri_em_register it worked perfectly, so I can't reconstruct what you did. Can you try running recon-all -autorecon2 -autorecon3 and see if it fixes things? Did the skull strip fail for you initially? Maybe em_register and the aseg stuff were run on a bad skull strip?
I'll attach the output of my mri_em_register run (called test.lta). You can compare it to the talairach.lta in that subject's transforms dir using tkmedit or tkregister2.
cheers Bruce
On Wed, 5 Oct 2011, Jeff Sadino wrote:
Hi Bruce, Thank you very much for taking a look at this for us. I uploaded it to your ftp server under the name JeffSadino_050089_S05.tar. About 70 of our subjects are showing similar problems. It seems to be happening more frequently in fs5 as compared to fs4. If you can find anything that will help, that would be great. Thank you again!
Jeff
On Wed, Oct 5, 2011 at 2:41 PM, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote: Hi jeff Sorry, this slipped through the cracks. If you upload the dataset we will take a look Bruce
On Oct 5, 2011, at 8:32 PM, Jeff Sadino jsadino.queens@gmail.com wrote:
Hello FreeSurfer Experts,Does anyone have any ideas about how to salvage this data?
Thank you very much! Jeff
On Sun, Oct 2, 2011 at 5:10 PM, Jeff Sadino jsadino.queens@gmail.com wrote: Hi Freesurfer Team, When we tried to process some subjects in FS 5.0.0 through the cross-sectional step in the longitudinal processing stream, we got inaccurate surfaces generated. Also, after doing skullstripping or adding control points and re-running the cross-sectional reconstruction, inaccurate pial and white matter surfaces were generated (see attached pictures). We are not sure how to fix this problem and this has affected about 70 of our scans. Several of these subjects we also processed in FS 3 and FS 4.3.1, and the surfaces were generated fine. Are there any known solutions to fixing the surfaces in the newer FreeSurfer? If not, then could we feed the 4.3.1 cross-sectionals into FS 5 to create the base template, and then use FS 5 to create the longitudinal reconstructions?
Thank you, Jeff Sadino
<050089_S05rhlh.png> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurferThe 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.