I don't know if it is appropriate or not. The use of the synth commands is experimental and I was not intending for anyone to use them yet. That's why I put in the FS_ALLOW_DEEP hook to act as a barrier. You obviously have the expertise to get past that barrier, but it put you into a no-man's-land that we do not support./

On 6/17/2024 10:33 AM, Dan Levitas wrote:

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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 <dgreve@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:

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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

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