Hi Dylan
I think you could probably do a recon without topology fixing although of
course the spherical mapping will then be multi-valued. It will take a bit
of hacking at recon-all to get it to work though as it is not a use-case
that we explicitly support.
cheers
Bruce
On Thu, 27 Feb 2020,
hs...@mskcc.org wrote:
External Email - Use Caution
Dear Freesurfers,
I am attempting to run the full reconstruction in Freesurfer on several
hundred patient images with diseased areas of the brain.
Without skipping any steps of the analysis chain, I am able to complete the
full reconstruction for about 50% of said patients. When the analysis is
able to complete, the disease sites are generally not included in the white
or gray segmentation labels, which is ideal for my use case. However, when
the disease is far from the cortical surface, it generally results in a
large topological defect. (In other cases, the Talairach check fails.) I
would like to know, does it really make sense to try to analyze the images
with a "real" topological defect, and if so, how to accomplish it?
I have tried to run the reconstruction with flags "-nofix" and
"-notal-check" to accept an imperfect Talairach transform and avoid crashes
trying to fix these unfixable topological defects. Unfortunately, the step
"mris_autodet_gwstats" which comes after "mris_sphere", seems to look for a
file "surf/lh.orig.premesh" which is not found, causing a crash. From what I
can understand, that file is produced by the so-called old topology fix [1],
so it would imply that a full analysis chain is not supported if you
eschew topology-fixing. Is this a feature, or do you recommend modifying
the logic of the script to work around it? This is as far as I got, but I
suppose there may be steps later in the analysis chain that will also look
for files only produced if the topology fix runs.
For your information, I am currently using the nightly build from February
12 for CentOS7, and I am amenable to switching to an older or newer build.
Thank you for taking the time to help me.
Best regards,
Dylan Hsu, Ph.D
Memorial Sloan-Kettering Cancer Center
[1] https://github.com/freesurfer/freesurfer/blob/6044b3df08de93c15e4b44807
349f21d9e4bc794/scripts/recon-all#L3128-L3139
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