Freesurfer only handles nifty-1 now.

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Patricia Pais Roldan
Sent: Thursday, December 14, 2023 8:17 AM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] cannot read nifti-2 files in freesurfer - files ok in AFNI

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Dear Freesurfer team,

I am having problems reading files with nifti-2 header, the error I get is something like "error: No such file or directory; error: niiRead(): bad number of dimensions (31488) in $file*". I get this error with any FS function (e.g., with mri_info $file), so I cannot work with these files in FS at all. The original files were nifti-1 (and readable by FS) but after processing them in AFNI, they were converted to nifti-2 (and now FS cannot read them). I contacted the AFNI team and everything seems to be alright with the files (AFNI functions can work with them and they can be displayed in the AFNI viewer). Does FS have the requirement of files being nifti-1?

Thank you very much in advance.

Best regards,
Patricia

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