Hi Lars – That’s correct, you don’t need to run cross-sectional TRACULA first, you just need to run longitudinal recon-all before you run longitudinal TRACULA, and it expects that the time points and base template subject IDs are the same for recon-all and for TRACULA. It sounds like the time points’ MNI registrations were not created, which is something that happens before the command that gives you the error. Is there an error in the time points’ trac-all.log files?
a.y
From: <freesurfer-bounces@nmr.mgh.harvard.edumailto:freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of "Lars M. Rimol" <larilin@gmail.commailto:larilin@gmail.com> Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Date: Saturday, July 29, 2017 at 8:31 AM To: FS maling list <freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu> Subject: [Freesurfer] longitudinal TRACULA
Hi,
I've run cross-sectional TRACULA on one subject, three different timepoints. Now I'm trying to run a longitudinal analysis on the same subject's 3 timepoints. My understanding was that for TRACULA, unlike for morphometry, I don't need to first run cross sectional before longitudinal, the only requirement is that I have a longitudinal dmrirc file that specifies the timepoints with their corresponding files.
It crashed with these error messages:
#@# Inter-subject registration (base template) lø. 29. juli 14:25:45 +0200 2017 cp /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat /work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_base/dmri/xfms cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/mni2anatorig.mat': No such file or directory cp: cannot stat `/work/projects/nn9208k/tbi/morfometri_test/DWI/TRACULA/long/1005_c1.long.1005_base/dmri/xfms/anatorig2mni.mat': No such file or directory Linux compute-16-32.local 2.6.32-696.3.2.el6.x86_64 #1 SMP Tue Jun 20 01:26:55 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
Any idea what went wrong here?
Thank you!
Sincerely yours,
Lars M. Rimol, PhD Senior Researcher Norwegian Advisory Unit for Functional MRI Department of Radiology St. Olav's University Hospital 7006 Trondheim Norway