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Hello FreeSurfer Developers,
I'm attempting to generate the segmentation files by running the "the recon-all" command. The command is failing and I am getting the below error.
ERROR: recon-all -s out_24 exited with ERRORS at Thu I searched and open the wm.mgz and other files using the below command following the tutorials: https://secure-web.cisco.com/1GbbXPOsSqlnYztwVk4vidqb-NyHGtLcthCKOl6FN_kuZ2l... https://secure-web.cisco.com/1Da47ZnOFHuJQ-ZILQdgpeHcwfKHsJb7cuOQe4WoXHMu9wP... Command: freeview -v out_24/mri/brainmask.mgz \ out_24/mri/wm.mgz:colormap=heat:opacity=0.4:visible=0 \ -f out_24/surf/lh.white:edgecolor=yellow \ out_24/surf/lh.pial:edgecolor=red \ out_24/surf/rh.white:edgecolor=yellow \ out_24/surf/rh.pial:edgecolor=red \ out_24/surf/lh.orig.nofix:visible=0
However, there are no surface files which are mentioned in the above command. The surface folder contains only the below files:
lh.defect_borders lh.defect_labels lh.orig.nofix lh.qsphere.nofix rh.defect_borders rh.defect_labels rh.orig.nofix rh.smoothwm.nofix lh.defect_chull lh.inflated.nofix lh.orig.premesh lh.smoothwm.nofix rh.defect_chull rh.inflated.nofix rh.qsphere.nofix
Please suggest on how should I modify the wm.mgz file in such case: Below are my doubts:
What I understood so far that wm.mgz contains information of white and non-white matter (whether gray matter or CSF), however I could see yellow color pixels of intensity 255 near the corpus callosum cavity which is non-white matter region, however when I modify the voxels in freeview using recon-edit option, I need to give 255 pixel value to the white matter region, I am a little bit confused on how to edit wm.mgz, whether to edit voxels in the white matter region with 255 value and erase in the non white region or do the opposite, Please guide.
What is the best way to modify the wm.mgz if the surfaces are not generated? Please advise.
1) FreeSurfer version: freesurfer-linux-centos6_x86_64-7.1.1-20200723-8b40551 2) Platform: ubuntu 3) recon-all.log: (PFA).
Thanks and Regards Sumit Sharma
------------------------------------------------------------------------------------------------------------------------------ Sumit Sharma