In that case, you should edits the wm.mgz (first web page) to find the
big defect. There are not any surfaces at this point because it did not
get that far
On 12/9/2021 3:53 AM, Sumit Sharma wrote:
External Email - Use Caution
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:
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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
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