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-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@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
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