Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

External Email - Use Caution

Hey Martin,

Sounds like a logical approach. I'll give it a try and let you know how it ends up.

I am using version 6.0 by the way.

Thanks,

Doug

-----Original Message----- From: Martin Reuter mreuter@nmr.mgh.harvard.edu Sent: Monday, September 16, 2019 2:39 AM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Douglas Merkitch dmerkitch@sralab.org Subject: Re: [Freesurfer] Longitudinal stream finalsurfs misalignment?

Hi Doug,

probably something went wrong during the editing. E.g maybe you edited files in the cross sectional or base directories and copied/saved these to the longitudinals or vice-verca. There should be no mis-alignments.

I would recommend this:

1. run one such subjects without edits through cross, base and long locally

2. if that looks good, run cross do finalsurf edits if necessary and complete cross runs. Then run base, do finalsurf edits and complete base run. Finally run long. All should be fine.

Depending on the type of problem you are editing, usually it is sufficient to edit these only in the base.

And make sure you use fs60 (not sure which version you used).

Best, Martin

On Fri, 2019-09-13 at 16:41 +0000, Douglas Merkitch wrote:

    External Email - Use Caution

Hey all,

I have a group of subjects with 2 time points that I've run thru the longitudinal processing stream. All goes OK until I run the recon-all -long and the resulting .long. subject dirs have the finalsurfs misaligned (i.e. one subject has the edits moved inferior and the other has them moved superior, causing drastic consequences to the pial/wm surfaces).

FYI these subjects were processed on a Linux-based high performance computing cluster and edits were made locally on a Linux virtual machine with subject dirs being transferred back and forth via scp. Not sure if this is relevant, but thought I’d mention it just in case.

I’ve uploaded a .tar file containing one of these longitudinal subject’s directories (i.e. both cross tps, base, and both resulting long tps) called ‘merkitch_upload_201980913.tar’ via the filedrop website.

Any help would be appreciated!

Thanks,

Doug

Douglas Merkitch Clinical Research Coordinator

355 E. Erie St, Chicago, IL 60611 312-238-5911 office dmerkitch@sralab.org

sralab.org

Facebook | Twitter | YouTube

Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer@sralab.org; and 3) delete and destroy all copies of the message and its attachments. Thank you. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Confidentiality Notice: This message and any attachments are only for the intended recipient(s) and may contain confidential, privileged and/or protected health information. If you are not the intended recipient of this message, please: 1) be advised that unauthorized review, use, copying, disclosure, or distribution is strictly prohibited and may be unlawful; 2) notify the sender of the delivery by reply e-mail or contact Shirley Ryan AbilityLab's Privacy Officer at 312.238.0766 or privacyofficer@sralab.orgmailto:privacyofficer@sralab.org; and 3) delete and destroy all copies of the message and its attachments. Thank you.