Hi Jamie

Where did the original .nii file come from? Seems like something might be wrong with it. Do you have the dicoms it came from you can try? What if you try to visualize the nifty directly?

Cheers Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu freesurfer-bounces@nmr.mgh.harvard.edu On Behalf Of Podell, Jamie Sent: Saturday, July 17, 2021 9:35 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon -all and mri_convert errors

External Email - Use Caution

External Email - Use Caution 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