Dear FreeSurfer group/Dr. Reuter,
My questions are in regards to the LONG stream.
My version is: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
1) Error message During the creation of the BASE, I get the following error in the beginning of the recon:
WARNING: Image geometries differ across time, maybe due to aquisition changes?
This can potentially bias a longitudinal study! Will continue in 10s.<<<< What should I be aware of in regards to this error?
The images were all acquired using the same MPRAGE protocol. All timepoints were fed MPRAGEs reconstructed in the axial orientation, but some may have been reconstructed at an angle. I was assured that this is not an issue for FreeSurfer, but could this be the reason for the error?
2) Conversion of LONG run aseg.mgz segmentations to native anatomical space
Executing the commands for converting aseg.mgz to native space (http://freesurfer.net/fswiki/FsAnat-to-NativeAnathttp://freesurfer.net/fswiki/FsAnat-to-NativeAnat) in the folder of a long run (me1.long.me_base) does not convert.
It seems to me that (unlike the cross runs) the long runs are all in the same space (in the template/ base space?) and their rawavg.mgz does not match that of the corresponding cross run. Some insight on this would be appreciated.
The question is how to convert an individual long run's aseg.mgz into native anatomical space. Perhaps using the rawavg.mgz from the corresponding cross run?
Thank you very much! Ivan
-- Ivan Kirov, PhD Postdoctoral fellow New York University School of Medicine Center for Biomedical Imaging 660 1st Ave, 4th floor, New York, NY 10016 Tel: 212-263-3337 Fax: 212-263-7541 ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================