Hi Dimitri,
Could you indicate the recon command that you ran? You could try rerunning the
recon-all command in the directory with one of the dicom files for the T1 image.
I’ve posted an example command below:
recon-all -all -i I50 -s Subj001
• The file after the “-i” flag indicates your input dicom file (I50)
• The file after the “-s” flag represents the output directory (Subj001) after
you have run recon-all
If you have more than one dicom file that you’d like to run through the recon
pipeline you can add -i flags for each additional dicom.
You can find additional information on the
Freesurfer<applewebdata://2215FD5C-E547-4E06-A0A9-A6F106A2BD18/that%20you%20can%20also%20locate%20on%20our%20Freesurfer%20wiki%20with%20additional%20explanation%20(https:/surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Practice)>
wiki
Let me know if you have more questions.
Best regards,
Ren
From: freesurfer-boun...@nmr.mgh.harvard.edu
<freesurfer-boun...@nmr.mgh.harvard.edu>
Date: Wednesday, January 6, 2021 at 21:34
To: Freesurfer@nmr.mgh.harvard.edu <Freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] Recon-all Error
External Email - Use Caution
Hello! I’m experiencing an error while I try to use recon-all in a T1 MRI
image, the following error message appears:
“[...]
using segmentation for initial intensity normalization
using MR volume brainmask.mgz to mask input volume...
reading mri_src from norm.mgz...
error:
mghRead(/home/developer/Desktop/BIBE_2020/Simulated_MRI/HC/rf0/t1_icbm_normal_1mm_pn1_rf0/mri/norm.mgz,
-1): could not open file
error: mri_normalize: could not open source file norm.mgz”
Thanks!
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