Sorry, I lost track of the original thread. Can you explain it or say why you are not running recon-all?

On 1/4/2021 9:27 AM, Camerino, I.L. (Ileana) wrote:

External Email - Use Caution Dear Douglas,

Thank you so much for your reply.

After trying: mri_em_register -mask brain.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta I got the following error: using MR volume brain.mgz to mask input volume... using top 50.0% wm points as control points....

== Number of threads available to mri_em_register for OpenMP = 1 == reading 1 input volumes... logging results to talairach.log reading '/opt/freesurfer/6.0/average/RB_all_2016-05-10.vc700.gca'... average std = 7.3 using min determinant for regularization = 5.3 0 singular and 841 ill-conditioned covariance matrices regularized reading 'nu.mgz'... mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/brain.mgz, -1): could not open file mri_em_register: could not open mask volume brain.mgz.

In fact the the file brain.mgz is not present in the mri folder.

I am a bit lost since I am getting a different error every time I try to solve the previous one and I do not understand what is the problem exactly.

The first error I got after running recon all on this subject (with a massive stroke on the left hemisphere) is a watershed error. So I added the control points and run: recon-all -autorecon2-cp -autorecon3 -subjid /project/3015068.01/ilecam/Reolang/Freesurfer/sub-056. After which I got the error:

mghRead(/project/3015068.01/ilecam/Reolang/Freesurfer/sub-056/mri/norm.mgz, -1): could not open file assuming input volume is MGH (Van der Kouwe) MP-RAGE using segmentation for initial intensity normalization using MR volume brainmask.mgz to mask input volume... reading from norm.mgz... mri_normalize: could not open source file norm.mgz

Finally to solve the above error I run: mri_em_register -mask brain.mgz -p .5 nu.mgz $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca transforms/talairach.lta but I got yet a new error: -1): could not open file mri_em_register: could not open mask volume brain.mgz.

Please could you let me know how can I understand what is the problem and how can I solve it?

Best regards Ileana Camerino

PhD candidate Donders Institute for Brain, Cognition and Behaviour

Centre for Cognition Spinozabuilding Room B02.25 Montessorilaan 3, 6525 HR Nijmegen The Netherlands Tel. +31-24 3612618

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