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

à The file after the “-i” flag indicates your input dicom file (I50)

à 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 wiki

Let me know if you have more questions.

Best regards,

Ren

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@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!