Hmmm, trying mri_convert file.nii.gz file.mgz

Then give file.mgz to synthstrip. I thought it would work with nifty, but maybe not?

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Salil Soman
Sent: Wednesday, April 5, 2023 8:11 PM
To: free surfer <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] synthstrip error

        External Email - Use Caution        

  Hi,

I am passing synthstrip an nii.gz file, and it keeps giving the error  "ValueError: cannot determine file format from extension for test " (full error below). Any suggestions on how to fix this issue? The nifti files was made from dicom images using dcm2nnix.

Thanks! 

Salil

Configuring model on the CPU
Running SynthStrip model version 1
Input image read from: test.nii.gz
Traceback (most recent call last):
  File "/usr/local/freesurfer/7.3.2//python/scripts/mri_synthstrip", line 245, in <module>
    image.save(args.out)
  File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/core/framed.py", line 274, in save
    save_framed_array(self, filename, fmt=fmt)
  File "/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/io/framed.py", line 136, in save_framed_array
    raise ValueError(f'cannot determine file format from extension for {filename}')
ValueError: cannot determine file format from extension for test