Dear Freesurfer experts,

 

I am running recon all as part of the tractography pipeline on a group of stroke patients.

This is are the first lines of my log file:

/opt/freesurfer/6.0/bin/recon-all -s sub-056 -i /project/3015068.01/ilecam/Reolang/Data/sub-056/MP2RAGE_denoised_roi.nii.gz -all -sd /project/3015068.01/ilecam/Reolang/Freesurfer/ -qcache

subjid sub-056

setenv SUBJECTS_DIR /project/3015068.01/ilecam/Reolang/Freesurfer FREESURFER_HOME /opt/freesurfer/6.0

Actual FREESURFER_HOME /opt/freesurfer/6.0

freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

 

Recon all did not finished successfully because a watershed error:

Sorting...

mri_watershed Error:

Problem in the COG calculation:

T1.mgz may not contain properly normalized white-matter.

Confirm that T1.mgz has enough white-matter voxels of value 110.

If white-matter contains few if any voxels of value 110, try adding wm control-points to nu.mgz, and re-run recon-all.

I added many wm control-points to nu.mgz and to T1.mgz but when I re-run recon-all I still get the same error.

 

Please can you help me to solve this problem?

 

Thank you in advance

Best regards,

Ileana Camerino

 

PhD candidate 

Donders Institute for Brain, Cognition and Behaviour

 

Centre for Cognition

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Room B02.25

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The Netherlands

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