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Hi,
I am trying to run recon -all on a T1 .nii file and keep running into errors. It says both "No such file or directory" and "bad number of dimensions." Since it seemed to me to be a problem with the .nii file, I tried running mri_convert separately but got the same errors. The file definitely exists in the location I designated (I can open it in freeview, etc.)... Do I need to manually change something about the .nii file to get it to run? Appreciate any help and am hoping there is a simple fix!
Here is what the log says:
/Users/jamiepodell/Desktop/PSH_MRI/008 \n mri_convert /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii /Users/jamiepodell/Desktop/PSH_MRI/008/mri/orig/001.mgz \n mri_convert /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii /Users/jamiepodell/Desktop/PSH_MRI/008/mri/orig/001.mgz reading from /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii... error: No such file or directory error: niiRead(): bad number of dimensions (10703) in /Users/jamiepodell/Desktop/PSH_MRI/s008_T1.nii Darwin Jamies-MacBook-Pro.local 18.7.0 Darwin Kernel Version 18.7.0: Tue Aug 20 16:57:14 PDT 2019; root:xnu-4903.271.2~2/RELEASE_X86_64 x86_64
Thanks, Jamie
Jamie E. Podell, MD
Assistant Professor
Division of Neurocritical Care and Emergency Neurology
Department of Neurology
Program in Trauma
University of Maryland School of Medicine