External Email - Use Caution Thanks, Doug.
I've spent some time trying to troubleshoot this issue, and have realized the following: 1). During the CROSS recon-all when I add -synthseg, no mri/transforms/talairach.m3z file is created in the CROSS folder. 2). During the BASE recon-all when no -synthseg is specified, a mri/transforms/talairach.m3z file is created in the BASE folder. 3). During the LONG recon-all (no -synthseg) specified, I'm able to successfully complete the process. Is this approach (specify -synthseg only for the CROSS recon-all) appropriate for longitudinal processing? On Mon, Jun 17, 2024 at 10:21 AM Douglas N. Greve <dgr...@mgh.harvard.edu> wrote: > Yes, that is the problem, not a lot of great options. One thing you could > try is to run synthmorph to create the m3z. > > On 6/10/2024 2:36 PM, Dan Levitas wrote: > > External Email - Use Caution > Hello, > > I am following the longitudinal freesurfer pipeline ( > https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial) > and getting this error on the final (LONG) portion: > > *ERROR: cannot find or read transforms/talairach.m3z * > > I can confirm that recon-all ran successfully during the CROSS and BASE > portions; it is only when I attempt to perform recon-all -long that things > fail. > > My suspicion is that CA registration was not performed during CROSS, as I > used -synthseg (and -synthstrip) in that recon-all command. I'm unsure if I > need to go back and specify -careg in the CROSS recon-all command (e.g. > *recon-all > -autorecon2 -careg*), or if there is some way to bypass this error. I > tried appending -nocareg to the end of my LONG recon-all command, but this > errored out with the following output: > > > > > > > > *mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta > /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta > sub-1000_ses-2pre.long.sub-1000 will read input aseg from > aseg.auto_noCCseg.mgz writing aseg with cc labels to aseg.auto.mgz will > write lta as > /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/transforms/cc_up.lta > reading aseg from > /N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz > error: > mghRead(/N/project/Kawata_TBI_1/R01_HighSchool_BIDS/derivatives/freesurfer/sub-1000_ses-2pre.long.sub-1000/mri/aseg.auto_noCCseg.mgz, > -1): could not open file* > > > Thanks for the assistance. > > Dan > > _______________________________________________ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://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 Mass General > Brigham Compliance HelpLine at > https://www.massgeneralbrigham.org/complianceline < > https://www.massgeneralbrigham.org/complianceline> . >
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