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:
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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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