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Dear FreeSurfer team,
I posted this question on October 21st but haven't gotten any responds back. I just wanted to follow-up on this and see if you can help me troubleshoot this.
Thank you and all the best, Ela ________________________________ From: Salar Dini, Elaheh elaheh.salardini@yale.edu Sent: Friday, October 21, 2022 2:18 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Subject: A TRACULA Question
Dear Anastasia,
Thanks for your support in the past few months. I got an error message in -prep step:
"Exception caught: itk::ExceptionObject (0x8a1e880) Location: "unknown" File: /home1/zs24/sandbox/build/ITKv5-install/include/ITK-5.0/itkSmoothingRecursiveGaussianImageFilter.hxx Line: 229 Description: itk::ERROR: SmoothingRecursiveGaussianImageFilter(0x8a1dd00): The number of pixels along dimension 2 is less than 4. This filter requires a minimum of four pixels along the dimension to be processed.
ConvertTransformFile 3 /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.txt --hm --ras file /home1/es2263/TRACULA/subjects_dir/37/dmri/xfms/diff2syn0GenericAffine.mat does not exist . Linux ursapet.med.yale.edu 3.10.0-693.el7.x86_64 #1 SMP Tue Aug 22 21:09:27 UTC 2017 x86_64 x86_64 x86_64 GNU/Linux
trac-preproc exited with ERRORS at Thu Oct 20 23:31:04 EDT 2022"
I am attaching a log file too. Do you have a guess why this happened and how we can address it? One possibility is that we don't have all the dMRI sequence slices (like 300 out of 1600 are missing).
Thanks for your time and help, Ela